My Little Pony: The Element of Space

Chapters

Chapter 1: Suspicions
Chapter 2: Sons & Daughters
Chapter 3: Two Paths
Chapter 4: Unknown Epidemic
Chapter 5: Khaoios Lives
Chapter 6: "Welcome Back, Marshall"
Chapter 7: Strategize
Chapter 8: The Secret Library
Chapter 9: Mystery of the Element of Space
Chapter 10: "Most Islands Hold Deadly Secrets"
Chapter 11: The Island of Mt Krokatani
Chapter 12: Confrontation
Chapter 13: Nightshade Illusion
Chapter 14: A Costly Victory
Chapter 15: A Father's Truth
Epilogue
Prologue

Chapter 1: Suspicions

Under the starry night sky, crickets chirped furiously, along the eastern coastline of Equestria. Crabs of all shapes and sizes scavenged for food at a nearby sand dune, where a strange structure laid, undisturbed. Looking for food, the crabs came across an orange crystal, shining dimly. Curious, they approached it, only to be blinded suddenly, with a force, pushing them away. In an instant, the beach shook, like an earthquake, only this was no earthquake. Something was disturbed.

As the mountain of sand exploded, ruins of a large, suspension bridge like structure were revealed, and there a bright light appeared. Stunned by it, the crustaceans witnessed something struggling to its hooves. Nearby, a passing Earth Pony walked over to the beach and noticed the bright light as it slowly dimmed. Seeing the animals near the mysterious light flee in fear of the creature, only for the light to dim to total darkness. Standing up on its four legs, the pony noticed, it was no ordinary creature. It was an Alicorn. At that moment, he tried to hide only to flee from the creature’s fearsome roar, as it echoed throughout the silent night.

Next morning, the Archivist and Doctor Hooves met, discussing the recent incident that could only leave both of them puzzled. Exhausted from their lack of sleep, they felt this situation was needed to be investigated.

“Madame Archivist. What was it you wanted to discuss, because I’ve too wanted to discuss the reappearance of Xenxus? The master informed me that he will alert the other masters about the situation, but…” Doctor Hooves was interrupted.

“Xenxus couldn’t have just reappeared in a blink of an eye on Equestria. He was locked up with Titannus and now I’m trying to figure out…wait.” the Archivist paused.

“What is it?” Doctor Hooves asked.

“I overheard in Canterlot that Tirek had escaped Tartarus because Cerberus left his post. However, I’m a little skeptic about that.” The Archivist said.

Suddenly the door opened widely. There stood General StoneColt.

“General? What are you doing here?” The both asked.

“No time to explain. I have two things to say.” The general said.

“Shoot” the Archivist replied.

“One. When Cerberus left his post, it wasn’t an accident. Xenxus lured him out, using himself as bait. The master informed me that a strategy like that was planned out, if they ever escaped.” The General spoke.

“How is that possible? Khaoios is the only one who could’ve done something like that. Xenxus is too…what’s the word I am looking for?” the Archivist replied.

“Stupid?” the General responded.

“If that’s what you would say, then yes. He’s not a strategic thinker, but more of on-the-spot.” The Archivist continued.

“So that means that Xenxus baited Cerberus out of Tartarus so only he could escape, which then freed both Tirek and…oh no.” Doctor Hooves replied.

“Yes. That means, Khaoios before he was imprisoned informed his brothers if something like that were to happen, he would tell them. He knew from the start that he was gonna be sent into isolation. However, that also means the escape plan wasn’t just for Xenxus…but for Titannus to escape. As for Tirek, it would’ve been highly unusual for them to escape together, so I can only guess when Titannus fled, Tirek followed behind quietly.” The General continued.

The Archivist slammed her hoof on the table in anger and annoyance.

“I TRULY CANNOT BELIEVE FOR THE LIFE OF ME THAT THIS IS HAPPENING. FIRST KHAOIOS, THEN XENXUS, AND NOW, TITANNUS. CAN THIS PLANET SUFFER ANY WORSE?” she yelled.

“Indeed, it can be a complete disaster, however that’s not why I am also here. From what we know Titannus is nowhere to be found, which is a relief. The bad news is…” General StoneColt paused.

“What…Khaoios’ body was found?” the Archivist responded rudely.

“Worse.” The General replied.

“Khaoios is alive?” Doctor Hooves said.

“Possibly. Yet, I haven’t had a chance to recon the area of interest.” The general continued.

“Possibly? No, no. Its either he’s alive or he’s not. How can you be?” The Archivist again rudely responded.

“Well excuse me, Librarian for not seeing correctly…” StoneColt scolded.

The Archivist got up and confronted StoneColt.

“What did you say, General?” the Archivist angrily said.

“I said…” StoneColt was interrupted

“That’s enough.” Doctor Hooves intervened.

“Fighting about this is not taking us anywhere. We need to get our acts together before this issue becomes severe.” He yelled.

Doctor Hooves calmed himself down
“Now, what do you expect us to do?” he continued, facing StoneColt.

StoneColt and the Archivist turned away.

“I need the pony that is able to communicate with animals. Apparently the witnesses are crustaceans and I don’t speak crustacean. Do you, old witch?”

“Why you!” the Archivist spoke under her breath.

“KNOCK IT OFF. THE BOTH OF YOU!” Doctor Hooves yelled.

The two stood silent. Doctor Hooves turned calmly to StoneColt.

“Let’s start from the beginning. Khaoios is possibly alive, first off. Now, what I am puzzled by is how he survived when we thought he was defeated?” he asked.

“That’s what I had thought.” The General replied.
“You know how Khaoios is. He, like his brothers can’t be defeated easily.” The Archivist intervened.

“Madame Archivist. We saw him plummet into the river. How could he have survived that?” General StoneColt said.

“Not to mention, he hates water.” Doctor Hooves added.

The Archivist rubbed her chin in worry.

“This is truly getting out of hoof. In the past few months we encountered Khaoios and just yesterday, Xenxus. Yet, speaking of Xenxus, I needed to get this out of my system. We need to determine, how he reappeared on Equestria, because as far as I can tell, I could not sense him.” The Archivist pointed out.

StoneColt and Doctor Hooves could only exhale in frustration. They both knew that the Archivist was correct and that the Bronco-Titans reappearance would only endanger the lives of all living creatures across Equestria, even outside its borders. There toughest challenge was yet to come. StoneColt turned to Doctor Hooves.

“Going back to what I had mentioned about the crustaceans. What is the name of the pony who is gifted into communicating with them? Basically, I need a translator for this.”

“Yes. That pony is Fluttershy. She lives in the cottage near the Clock tower. In addition, I request that you take Rainbow Dash with you. Both of them will be of good use since they are both Pegasus ponies.” Doctor Hooves recommended.

“Ah. The one who is known as the “Best Flier” in Equestria. This should be quite interesting. As for the other one, I will speak with her.” General StoneColt said as he walked to the doorway.

“One thing, General. Make sure Rainbow Dash does not go overboard by challenging you know who?” The Archivist said.

“She has the tendency of showing off…” she continued.

“Oh I know. And one thing for you…get some rest. I merely tested your stress level and it’s bad.” StoneColt scoffed, as he walked out.

The door shut behind StoneColt.

“Sometimes I ask myself, what did Paguseus teach his apprentice, but that’s for another time.” The Archivist said.

Doctor Hooves turned to her.

“What must we do?” he asked.

The Archivist knew that this threat would need to be alerted. She responded that Twilight will need to be informed as well as the other Princesses. However she felt that it will once again be another stressful mission for Twilight, but had no choice. The Archivist at this point began to question herself about this secrecy, she and her colleagues promised to their masters, but with the return of each of the Bronco-Titans, it puzzled her. Without a word, she walked to the doorway.

“Doctor. I may be severely penalized about this however we must reveal the whole truth to the Princesses. These conspiracies and secrets we have been withholding is only making matters worse for everypony. Even ourselves. But…I just don’t know what to do” the Archivist sadly responded.

Doctor Hooves sighed.

“I know exactly what you mean. In the meantime, let’s only worry about what is going on, and leave the rest aside.” He insisted.

“Very well, then…” The Archivist replied, only to be knocked back unexpectedly.

Suddenly, a mysterious pony appeared, falling on top of the Archivist. Unlike other pony’s, this particular pony had purple Crystals for a tail. She was purple and spoke very innocently.

“Oh I’m sorry. Are you the one they call, Madame Archivist?” the pony asked.

The Archivist looked up and recognized something unusual. This pony was way too familiar only to turn to Doctor Hooves. She then turned back to her.

“Yes, young one. I am the Archivist. May I ask what you are doing here…Amethyst Crystal?” The Archivist said.

Doctor Hooves’ eyes widened.

“Khaoios’ daughter?” he gasped in shock.

Chapter 2: Sons & Daughters

Over at Fluttershy’s cottage, General StoneColt stood by the doorway and knocked.

“Miss Fluttershy? Are you there?” he called out.

“Wait a moment, please.” Fluttershy responded.

From outside, StoneColt could here rustling, with pans falling on floor, barking, chirping, anything he could think of that involved animal sounds. After a minute, Fluttershy opened the door, walked out, and closed it behind her.

“Oh please excuse me about that. The animals have been acting very strange lately. Like something they could sense that we can’t.” Fluttershy said.

“I see…looks like you have a zoo for a house.” He commented.

“Yes. I do.” She chuckled.

StoneColt cleared his throat.

“Anyhow, I wanted to ask you are animals are able to sense earthquakes much faster than any other creature?” he asked.

“Yes. They are capable of doing that. Why do you ask?” Fluttershy asked.

“I see…well, I am in need of your assistance.” StoneColt commented.

“Sure. What do you need?” Fluttershy asked.

“Have you ever come across Crustacean creatures before?” StoneColt asked.

“Like crabs. Unfortunately no, but I may be able to understand them. Why?” she asked.

StoneColt took a moment to absorb her words.

“I need you to translate what they are saying. Apparently word has it that something appeared on the beach line, near Manehattan and the witnesses were crustaceans. I can’t understand them, which is why I need you to tell me what exactly they saw. Do you understand what I mean?” StoneColt said.

“Of course. When will I meet them?” Fluttershy happily replied.

“We will meet them in two hours. In the meantime, can you please get your friend, Rainbow Dash? This will concern her as well. Once you have done with…um…whatever you are attending to, meet me at the city square.” StoneColt ordered.

“Yes sir.” Fluttershy replied, going back into her home.

As StoneColt walked away, he felt confident that both the Pegasus Mare’s will do their part, but something wasn’t right. Ignoring the matter, he continued back to Ponyville. Back at Doctor Hooves’ home, Twilight had arrived and was introduced to Amethyst Crystal. Explaining the current situation, the Archivist still couldn’t understand why Khaoios’ only daughter would come to her for answers. Twilight turned.

“Let me get this straight. Your father, Khaoios, who literally raged havoc on Equestria…is back? Do you have any idea what that monster did…” Twilight was interrupted.

“My father is NOT a monster!” Amethyst Crystal shouted.

The Archivist walked over, putting her hoof on Amethyst’s shoulder.

“I know how protective you are of your father, however he did commit crimes, including blackmailing the princess, into giving him knowledge of the Guardians.” She said.

Amethyst’s ears dropped.

“I know. It’s just the first time I heard about his return, I just couldn’t face him. I…I…was scared.” Amethyst replied, innocently.

Doctor Hooves, the Archivist, Twilight understood how she felt, but could do no good to cheer her up. They knew Khaoios was dangerous and to reason with him, would be hopeless. There was a long silence in the room, until a knock was heard. The Archivist opened the door to realize it was six Pegasus ponies, landing on one another as they entered the house. Doctor Hooves slammed his hoof against his face.

“Family reunion now?” he said.

The oldest of the six stood on his hooves.

“Forgive us, Madame Archivist, Doctor, and Princess. The General sent us here, and…wait…what Amethyst is doing here?” the he asked.

“Now, Mariner let’s not get worked up.” Doctor Hooves commented.

“No. It’s not that. I was also told by General StoneColt to meet him at the city square. I didn’t expect him to call her for assistance.” Mariner replied, pointing at Amethyst.

“Wait what’s going on here? I thought it was you that sent me a message requiring my presence.” Amethyst asked the Archivist.

Commotion between the ponies broke out as the crowd kept getting louder and louder. Twilight stepped in.

“Now wait…wait. Let’s all calm down, please. First off, the Archivist and Doctor Hooves just sent General StoneColt to see my friend, Fluttershy. Then, he’ll go to the city square. We can all meet him there.” She spoke.

“That’s sound like a better plan. Aye?” one of the other Pegasus pony said.

“Very well…now before we go anywhere, can I ask for your names? Don’t think I’ve met any of you before.” Twilight responded.

The Archivist stepped in.

“I can be of assistance with that. Iron Clads, Attention!” The Archivist yelled out.

Then the Pegasus ponies lined up like a military squad. The Archivist ordered each one to step forward and give their names.

“Greetings, Princess! I am Mariner, first son of Interstellar Paguseus” Mariner spoke.

Another walked up.

“Hello, Princess! My name is Deep Impact, second son of Interstellar Paguseus. Friends tend to call me Impact, for short.” Deep Impact said.

“Hello, Princess! Names Orbiter, third son of Interstellar Paguseus!” Orbiter said.

The next Pegasus pony walked up as if he were trying to show off.

“Hey there, Princess! Names Moonraker, fourth and cool son of Interstell…” Moonraker was interrupted.

“That’s enough, lover boy.” One female Pegasus said, pulling Moonraker away.

“Forgive me Princess. He has the tendency of showing off.” She continued.

Twilight giggled for the moment.

“No worries. My friend Rainbow Dash is like that…” she said.

“Really? Is she cute?” Moonraker commented.

“MOONRAKER!” Mariner yelled.

“Sorry, bro.” Moonraker apologized.

Twilight continued to giggle. In her mind, Twilight found Moonraker rather cute.

“May we please continue…?” The Archivist spoke.

“Yes. Hello, Princess! I am Voyager, fifth son of Interstellar Paguseus.” Voyager spoke.

The female Pegasus pony stepped forward.

“Salutations, Princess Twilight. My name is New Horizon, first daughter and sixth child of Interstellar Paguseus.” She spoke.

Twilight after hearing the introductions looked at all of them.

“You’re all siblings? That’s so cool, in my opinion.” Twilight asked in curiosity.

“Depends…” Mariner spoke.

“Depends on what, Mariner? She finds us…you know…cool. Probably because she likes me…” Moonraker smirked.

“Oh please, shut up, Moonraker.” Orbiter said under his breath.

Twilight began to blush. She cleared her throat.
“So there six of you?” she said.

“Not all of us, to be honest.” Mariner sadly replied.

Twilight tilted her head, curiously. The Archivist and Doctor Hooves on the other hoof realized what they meant. They were missing their youngest sibling, who was nowhere to be found. Growing up with a missing sibling took a toll on them emotionally.

“Crying about something that occurred in the past isn’t gonna get us anywhere.” StoneColt spoke appearing at the doorway.

“Now that we’re all here…well…almost everypony, let’s go to the square, shall we?” StoneColt spoke.

They all understood as they walked out of Doctor Hooves’ home. As they made it to the town square, Fluttershy and Rainbow Dash had awaited.

“What took you guys so long?” Rainbow Dash called out.

Moonraker hearing her voice, sent him into a trance. Orbiter turned.

“What’s wrong?” he asked.

“Her…she’s beautiful”. Moonraker responded, still tranced.

New Horizon bit Moonraker’s ear.

“Ow! What was that for?” he yelled.

“Show some respect, cool boy.” New Horizon giggled.

Rainbow tiled her head.

“Um…what’s up with that guy?” she asked.

“Oh…he’s just wants to be cool for you.”

“Really…” Rainbow Dash smirked.

New Horizon rolled her eyes, annoyed with her brother and his immaturity. At the same time she felt worried about him, even though he was older than her. StoneColt face-hoofed himself.

“Kids…why did I take the responsibility of being their “uncle”?” he thought to himself.

“Maybe because Paguseus noticed how hard headed you are that he wanted to see how well you can handle kids? Wouldn’t be surprised if he’s testing you.” The Archivist chuckled.

“Ha…ha…ha. Very funny” StoneColt replied sarcastically.

“Anyhow, see we are all finally here…here’s the mission. I’ve been scouting around the eastern seaboard and learned that something had caused some commotion and we want to keep the public out of it the best we can. The mission is to go to this area of interest along with our animal lover-slash-translator, she will tell us what these animals have seen…”

“You can talk to animals. Wow…that’s awesome.” Voyager spoke proudly.

“Keep your hooves on the ground, V” StoneColt replied.

“Now, Princess Twilight. I would like you, the Archivist, and Amethyst to go to Canterlot and await our message. In the meantime, we will depart, but I would like you first to tell you’re three other friends to monitor progress here. Is that understood?” StoneColt ordered.

“Yes, sir.” They all responded.

“Alright then. Let’s move out.”

“Roger!” they replied.

Chapter 3: Two Paths

Splitting up, StoneColt walked out of Ponyville with Fluttershy, Rainbow Dash, and the others. Twilight, the Archivist, and Doctor Hooves went to visit Applejack, Rarity, and Pinkie Pie. However, far above Equestria, a shadowy figure appeared, watching them like a hawk seeking its prey. Within seconds, it disappeared. Sensing an unusual presence the Archivist turned and looked up. Observing the area, she turned back without worry and proceeded. Soon the three arrived at Sweet Apple Acres where Applejack and Applebloom struggled to remove termites from one of their special apple trees.

“Dang, Termites. They’re eatin’ up my tree.” Applejack struggled.

“Yeah…and them apples as well. We don’t even know where they came from?” Applebloom commented.

Twilight observed the tree and noticed the termites were black and had orange spots on their backs. She rubbed her chin.

“Strange that I’ve never seen these kind of termites before…” she said.

“Let me see.” Doctor Hooves said as he walked up.

He observed the termites with a magnifying glass he had in his pocket. He spent a few minutes still observing the insects, but it was no good. That is until he noticed the spots on their backs, which he back away fast.

“Madame Archivist…you should see that?” Doctor Hooves said, handing over the magnifying glass.

She looked at him and observed his facial expression as if he saw a ghost. Curious, she took the magnifying glass and glanced at one termite with the orange spots. After studying it for a few minutes, she turned to Applejack and Applebloom.

“Ladies…do you know when you first came across this? Also, did you get any on your body?” she asked.

Applejack and Applebloom looked at one another.

“Ummm…yeah. We did get a few on us. Why? Are we gonna get cursed like that Poison Joke Plant?” Applejack said.

“No. I just want to make sure. And the time?” The Archivist replied.

“This morning.” Both Applejack and Applebloom replied.

“Madame Archivist…if I may…Girls, just as a precaution, please wash up.” Doctor Hooves stepped.

“O...K…” the both sisters said as they left the tree alone.

“Go with them Twilight. This is one of those times the Doctor and I need to have a little talk.” The Archivist mentioned.

“Sure.” Twilight responded following Applejack and Applebloom.

As they walked into the barn, Applejack turned to Twilight.

“Um…Twi, who’s that pony with the purple crystals on its tail. I’ve never seen her before?” Applejack whispered.

“I’ll tell you later. But, she is the daughter of Khaoios.” Twilight replied.

“SHE’S WHAT?” Applejack jumped.

Twilight closed Applejacks mouth to keep her quiet from the incident. The Archivist turned to look at the two, only to smile nervously. As they walked inside, Amethyst head dropped.

“Why do ponies treat me like I’m a demons daughter? I’ve done nothing wrong and they look at me like I’m no pony.” She sadly responded.

“Don’t do that to yourself, my little pony. They have much to learn, because as it stands your role will be very useful and thus you will become some pony of importance to them. Give it time for them to absorb your appearance as watch as they become much friendlier to you. Not to mention, if you want to understand the meaning of friendship, try staying close to them. When you learn from them, they will learn from you. I promise.” The Archivist replied.

Amethyst wiped away her tears, smiling. The Archivist smiled back, then turned to the infected tree. Doctor Hooves continued to study it, but could only come up with questions.

“Which one of the Bronco-Titans were capable of infecting trees with the use of termites. I’m beginning to believe this was Khaoios’ doing, but I doubt that.” She said.

“Xenxus perhaps. He is somewhat of a walking plague because of his sulfuric dioxide he breathes.” Doctor Hooves mentioned.

“Possibly. Let’s just hope that it’s nothing but normal termites biting for food.” The Archivist commented.

“I know what you mean.” Doctor Hooves said.

From the barn, Twilight, Applejack, and Applebloom peeked out, wondering what they were talking about. Taking it as somewhat of a joke, Applejack and Applebloom continued to their room for towels. Twilight looked out again but she didn’t take this as a joke. Something was up.

As they investigated the infected tree, StoneColt along with the other ponies continued their way to the coastline. On the way, Moonraker flew up to Rainbow Dash.

“So, Rainbow Dash. I hear you like to do “cool” things. Like sports, games, other things, if you know what I mean…” he said.

“Are you kiddin’? I love playing sports and games. Oh…Oh do you race my wings could use a nice stretch.” Rainbow Dash commented.

“Hey yeah…I sure know how to race.” Moonraker spoke boastfully.

“Pfft…you? Race? Moonraker, our brother, you are reckless when it comes to racing.” Mariner commented.

“Good in other sports, but racing…yeah…okay…” Orbiter replied.

“What?! I AM A GOOD RACER! I’m the best one out of all of you! I even proved it!” Moonraker yelled.

“Moonraker…the last time you raced, you hit a barn…” Mariner said.

“…then Moolissa…” Deep Impact continued.

“…then the window…” Orbiter continued.

“…then the mailbox…” New Horizon continued

“…oh wait…it gets better…the grand finale…Ol’ Stall’s rocking chair. Oh I remember his face when you broke his chair. Hilarious.” Voyager laughed hysterically.

“Oh golly…you thought it was funny. I had to pay for that chair so I shouldn’t be talking or laughing, Voyager!” StoneColt said loudly.

Moonraker laughed.

“That includes you, moron!” New Horizon yelled.

“Why you…” Moonraker snared.

“Nah…he’s cool to me.” Rainbow Dash said, putting her shoulder over Moonraker.

“Alrighty. Last one to the beach is a rotten egg!” Rainbow Dash flew away laughing.

“Oh you are so on.” Moonraker said making chase.

The remaining siblings followed them as fast as they could with Fluttershy and StoneColt behind. StoneColt sighed.

“Funny, they are all your ages, but Moonraker acts like a foal. But one thing he does maintain is his loyalty to his siblings.” He commented.

“Oh don’t worry. Rainbow Dash is exactly the same thing. She likes to show off a lot, but is always loyal to her friends. Not to mention, as much as she looks out for me, I look out for her. Same as New Horizon from what I saw.” Fluttershy replied.

“Hmm…I see. Perhaps you’re right. Now let’s hurry.” StoneColt said.

“Of course.” Fluttershy replied.

Chapter 4: Unknown Epidemic

As StoneColt and the group of ponies continued their route to the coastline, screaming was heard within Rarity’s house.

“Oh my goodness. Ants…ANTS!!! EVERYWHERE!!!” Rarity screamed out.

Twilight, Applejack, The Archivist, Amethyst, and Doctor Hooves moved their eyes left and right, as Rarity ran back and forth, trying to save her clothing.

“Umm…Rarity. We need to talk.” Twilight called out

“NOT NOW TWILIGHT!!! I MUST SAVE MY FABRICS!!!” Rarity yelled.

“The ants are not going to stop. Applejack’s trees were filled with termites and I have a feeling it will continue…” The Archivist said.

Rarity ran up to her, confronting her.

“TERMITES!!! NO!!!!!” she yelled.

“RARITY!!! PLEASE STOP YELLING!!” Twilight yelled.

Suddenly, the ants crawled out of Rarity’s house, shocking the ponies.

“What just happened?” Applejack asked curiously.

“I have no idea…” Twilight replied.

Doctor Hooves turned to the Archivist.

“Let me go to the lab and analyze the termites and these ants. Not an common behavior, I’m guessing.” He said.

The Archivist agreed and Doctor Hooves left the house. In the process, The Archivist assisted Applejack, Twilight, and Rarity as they clean up the mess. Dusting the fabrics, floors, and other items the ants dropped on the floor, Sweetie Bell walked in.

“Oh hi, Rarity! What’s going on here?” she asked.

“Oh nothing, sweetie. Just…doing some cleaning along with everypony else.” Rarity nervously responded.

The facial expression of the other ponies, made Sweetie Bell curious. Tilting her head, Rarity tilted hers like a parrot.

“Ok! Just want to let you know that Scootaloo, Applebloom, and I are gonna hang out for a while. See you later!” she jumped.

“Ok. Bye.” Rarity continued to smile nervously.

As the door shut, they all breathed a sigh of relief. Rarity at that moment couldn’t handle telling Sweetie Bell what just occurred. Instead, she wanted to leave her out of it, considering to be a wise decision, the Archivist thought. After spending half an hour cleaning up, they decided to visit Pinkie Pie, which they soon realized her visit would be something of a surprise. Walking into her home, they noticed locusts flying around.

“Pinkie Pie! Where are you?” Applejack called out.

Pinkie Pie jumped out of a corner, where military gear.

“Hurry!” she yelled, grabbing the four and pulling them behind the counter.

It surprised them to see Pinkie Pie was having a similar issue. Something was very unusual and needed to be solved immediately, the Archivist thought. Suddenly, Rarity screamed loudly which then halted the Locusts. There was a silence in the house, until the swarm flew out of the window and disappeared into the Everfree Forest. Pinkie Pie walked out with her jaw dropped?

“What just happened?”

“Believe us, darling. We asked the same question in my house.” Rarity replied.

“Hold on ya’ll. First the termites on the apple trees, then the ants in Rarity’s house, and now locusts? Is there something we should know about, Madame Archivist?” Applejack asked curiously.

Archivist shook her head, having no answer. Twilight began to think about the three incidents as well, thinking back to the time they first encountered discord. However, he was only spreading disharmony from one thing to the other. This was all of a sudden, happening at the same time. She turned to the Archivist.

“Since we are all here, what was it you wanted to discuss?” she asked.

“Yes. Besides questioning myself about this issue, I would like us to go to Canterlot and explain the current situation. The incident over in the coastline plus what we just encountered here. Seems that some secrets can no longer be hidden. If we keep this up, we would only bring danger to ourselves.” The Archivist mentioned.

Twilight finally realized the Archivist was starting to sense dangers and that her idea of keeping secrets is doing no good. Yet, at the same time she agreed that these incidents must be brought up to the Princesses.

“Will Princess Cadance be there as well?” Twilight asked.

“Yes. It will concern her as well, because the Crystal Empire is a vital area of interest.” The Archivist replied.

“Then let’s head on up there to Canterlot!” Applejack said.

They agreed and headed for the Train Station, nearby. As they got on board the train, a faint whisper was heard. The Archivist and Twilight turned.

“Do you hear that?” Twilight asked.

“Yes…faintly.” The Archivist replied

“What does it mean?” Twilight asked again.

“Keep your eyes peeled, Princess. We’re being watched…” The Archivist cautiously responded.

As they entered the train, high above the clouds a shadowy figure stared before disappearing. Finally reaching the shoreline, the group of ponies halted in shock after seeing seagulls, crabs, and some fish laying on the sand, sick. Fluttershy hurried over to each one.

“Oh my goodness. Are you okay?” she asked calmly.

The birds she picked up were breathing heavily, but alive. She noticed their temperatures were high enough, giving them a possible fever. StoneColt turned to the other ponies.

“Search around and assist Fluttershy with these creatures, I’ll scout ahead and see what I can find.” He said taking flight.

Moonraker flew at Rainbow Dash’s side.

“Don’t worry, we’ll be perfectly fine.” He said.

“Oh here we go again.” StoneColt rolled his eyes.

“No snoody business from any of you. Understand!” StoneColt yelled.

“Yes, Sir!” They all replied.

As StoneColt went further up the coastline, New Horizon could not believe her eyes at what she was seeing.

“These poor creatures…they seem to be in some sort of shock? Mariner, what do you think?” she commented.

Mariner walked over and observed the animals shaking. Then he checked their body temperature which he realized was unusual. He picked up his head and turned to his sister.

“There in severe shock. It’s like whatever they saw scared them to a point of fainting.” He spoke.
Curiously on what he said, Fluttershy walked over to him.

“Um…just out of curiosity, what you do?” she asked.

“Rarely asked, to be honest, but besides being a navigator, I am also a veterinarian. Something similar to what you do, but only a little more advanced” he winked.

“Oh, that’s so great. Can you teach me something things you do? I adore animals, but I never knew there would be other ponies with the same interest.” Fluttershy responded happily.

“Um…can we please continue? I’ve got a few crabs over here that are covered with something.” Orbiter called out.

Both Mariner and Fluttershy gathered all the injured animals, while Voyager and New Horizon set up a campfire to nurse the animals back to health. Flying over to Orbiter, they noticed the crustacean creatures were covered in orange spots. When Fluttershy went to lift one up, Mariner put his hoof in the way. He informed that the spots maybe somewhat venomous if touch. It was better to get protective gear to lift them to the campsite. Suddenly, Voyager appeared with a bag and dropped it on the crabs.

“Pick them up just like that and come on over.” Voyager said.

Using the bag to pick up the crabs and heading back to the campsite, StoneColt continued his view of the coastline, seeing nothing but rocks and sick animals. It was like an epidemic occurred on the shoreline. Flying back to the group, Moonraker and Rainbow Dash managed to pass by informing him that no other sightings of animals other than the ones StoneColt found. Good news at that point was that the animals were all and alive, and required medical attention. Heading back to the camp, New Horizon and Deep Impact prepared water and food.

“I gotta admit, this is seriously weird. How could something like this occur on these animals? It’s like the Pony Pox all over again, only this one is affecting other species.” Deep Impact commented.

“I wish we could understand them at least, so it would be easier to find out what did this to them.” New Horizon mentioned.

“Do not worry. We have just that.” StoneColt replied, turning his head to Fluttershy.

“Of course, let’s first nurse these poor things back to health and ask them.” She replied.

Chapter 5: Khaoios Lives

While the ponies nursed the animals back to health from an unknown epidemic, Twilight, The Archivist, Applejack, Rarity, Pinkie Pie, and Amethyst Crystal entered the throne room in Canterlot Castle. There, Princess Cadance and Twilight’s brother, Shining Armor stood.

“Twilight! You’re here!” Cadance said happily.

“Cadance! Shining Armor!” Twilight replied.

“Twily. It’s so good to see you!” Shining Armor said.

Twilight ran up to them, hugging them. Behind, Princess Celestia and Princess Luna appeared.

“Hello, Princess.” Princess Celestia said.

“Greetings, Princess.” Princess Luna continued.

“Now that we are all here, what would you like to talk about within this meeting, if I may ask? Princess Celestia asked.

“Well…umm…” Twilight turned to the Archivist.

“I was informed by General StoneColt Hoover, that something was apparently disturbed on the eastern seaboard of Equestria. Thus they are investigating the area as we speak.” The Archivist said, walking forward.

Princess Celestia and Princess Luna felt skeptic, however Twilight agreed that something did occur. Not only their but in Ponyville.

“When we saw Fluttershy, she told us that the animals were being frantic and were somewhat uncontrollable. She said that this behavior they should was very unusual and had to do with that incident over in the coastline.” Twilight continued.

“What else did this problem cause?” Princess Luna asked.

“Termites infected my apple trees…” Applejack commented.

“Ants destroyed my fabrics…” Rarity continued

“…and Locusts attacked my cakes! MY CAKES!!!” Pinkie Pie yelled in horror.

Shining Armor squinted.

“That is interesting. Just this morning, both Cadance and I found mice running throughout the Library in the Crystal Empire. It was like they were…” Shining Armor paused.

“Like what?” Twilight asked.

“Like running away from something. We tried to gather them together, but as we did they just continued to run away. It was as if they were afraid of us, when we weren't trying to hurt them. We were only trying to help but once we tried again to bring them together, they just fled the Empire.” Cadance continued.

Princess Celestia turned to Princess Luna.

“Luna, didn’t you have bats flying in your room?” she asked her sister.

Princess Luna’s eyes widened, realizing that they weren’t alone on the issue.

“Indeed, I had last night. It’s interesting that this epidemic is causing animals to respond in fear. It's like they can sense things that we can't. What should we do?” Princess Luna replied.

“I don’t know. What would you recommend, Madame Archivist?” Princess Celestia said.

“Well, as of now I don't know. So let’s work step by step on solving this matter.” The Archivist said.

That evening, Fluttershy along with the other ponies managed to nurse most of the sick animals back to health. As some StoneColt called her over with a crab.

“I need you to tell me what he said, Fluttershy.” He said.

“Yes.” Fluttershy replied.

“Hello there, little friend. Would you please tell me exactly what happened?” She asked.

The crab was speaking, making clicking sounds that no pony other than Fluttershy could understand. For a while, it puzzled them.

“Do you know what she’s sayin?” Moonraker whispered to Rainbow Dash.

“She’s done this before. Even I don’t know what its saying.” Rainbow Dash replied.

“Oh…you saw it?” Fluttershy said.

“Saw what? What did he say?” StoneColt jumped.

At Canterlot, the Archivist explained the situation, and thus asked about the animals having some sort of discoloring on their bodies. Princess Luna stated the bats had orange spots, unlike she has seen before. Over in Ponyville, Doctor Hooves examined a specimen of a termite, covered with orange spots, until something shocked him. Curious, he took another specimen to his lab. Back on the coastline, the crab continued to inform Fluttershy that something awoke and attacked them, and that it came from a stone.

“An Orange Stone…that looked like a crystal.” Fluttershy said.

StoneColt’s eyes widened.

“No…it can’t be.” StoneColt said.

Up high in the Wonderbolts academy, a shadow appeared near one of the alley ways walking towards the light. A young Pegasus recruit went to retrieve a football at that moment, and slowly looked up.

The Archivist, over in Canterlot, jumped after hearing the bats where covered in orange spots. She quickly stood up and asked, did any of them look “crystallized”. The four Princesses tilted their heads, curious about what she said. Princess Cadance stepped in.

“When we had mice, they were crystallized with orange spots. Why?” she asked.

StoneColt asked Fluttershy if that is all the crab knew, until she turned.

“The crab said that they came across something in the south, not too far from here. He said it looked like a big building or something.” Fluttershy said.

StoneColt, now nervous flew as fast as he could down south to a wreck. Only to come across another big shock. At Ponyville, Doctor Hooves examined the termite, only to notice it wasn’t a termite at all. It was a crystal rock that cracked his microscope. Yet a small explosion occurred after he examined it, sending him back into a desk. After Cadance informed them about the crystallized mice, the Archivist stood up.

“If they were covered in orange spots…” the Archivist said.

“…and they were crystallized…” Doctor Hooves commented.

StoneColt observing the wreckage came across a crater with pieces of an orange crystal spread all over the ground. Then, he looked up to notice the structure was remains of a suspension bridge. Immediately he realized, this is no ordinary creature the animals encountered.

“…this bridge…the crater…the crystal…that means…HOLY FISH!!!” StoneColt paused.

At the Wonderbolt Academy, the Pegasus pony looked up and suddenly ran out of the alley. The creature raised his wings, glowing bright orange, creating an explosion in the alley. Within seconds, an S.O.S was sent as explosions rocked the Academy like a powerful earthquake as the creature appeared on top of one of the buildings. The Wonderbolts looked up and gazed at an alicorn. It was a familiar face.

“Hello, ponies. Did you miss me?” the alicorn smiled sinisterly.

From all directions, The Archivist, StoneColt, and Doctor Hooves stood up, with her eyes widened, sensing exactly who it is.

“KHAOIOS!” they gasped.

Chapter 6: "Welcome Back, Marshall"

At that moment, all their theories were proven wrong; the creature they thought they had destroyed walked once again. Suddenly, a Royal Guard ran into the throne room, exhausted.

“You majesty! News from Cloudsdale. Reports say something is attacking the Wonderbolts Academy!” he quickly spoke.

The Princesses turned to one another. They have fallen for another trap by the Master of Intelligence, himself. Quickly, Princess Celestia and Princess Luna issued a squad to assist. Twilight, the Archivist, Applejack, Rarity, Pinkie Pie, and Amethyst Crystal quickly turned to one another.

“Let’s go.” Twilight said.

Princess Celestia and Princess Luna informed Twilight that they, along with Princess Cadance and Shining Armor will remain at the Castle to keep it under guard from Khaoios. Agreeing, they left for the Wonderbolts Academy. Back on the coastline, StoneColt quickly flew back to the group.

“We need to go, NOW!” he ordered.

“What happened?” Fluttershy and New Horizon asked.

StoneColt turned.

“Khaoios is back.” He replied, flying as fast as he could to the Academy.

At the Wonderbolt Academy, bright orange lightning bolts rained down, striking almost everything in its path. Explosions from Khaoios power, shook the ground like a massive earthquake. The Wonderbolts maneuvered lightning bolts unleashed by the Bronco-Titan, however they were no match for Khaoios’ power. Captain Spitfire and her squad flew back and forth, like planes trying to take down a giant monster. Only thing was, this was a smart “monster” in her opinion. Every move they made, he would only dodge it and hit them where they would least expect it. Their weak spots. Dropping like flies, Khaoios continued his rampage, walking on the runway.

“You pegasi are pathetic. Do you really think your incredible agility can beat me? An alicorn capable of predicting your next moves. Huh…I pity your intelligence.” Khaoios boasted.

Soarin, who managed to appear from the top, hit Khaoios, but only realized he made a mistake. Khaoios turned and snared.

“Let me show you true speed, wretch.” Khaoios said, as he flew up high in the sky, then quickly slammed on to the ground.

The shockwave cracked the asphalt, knocking ponies off their hooves. They knew they were in complete disarray. Soarin, who happened to be on Khaoios’ back, was thrown off and knocked out temporarily. Witnessing the devastation Khaoios was already causing Spitfire and Fleetfoot raced at full speed, only to be knocked away by Khaoios powerful wings. Suddenly, out of nowhere, a Pegasus appeared catching Spitfire and Fleetfoot.

“Gotcha!” The Pegasus said.

Spitfire looked up and noticed it was the same Pegasus that saved her in Manehattan. Lowering them down, he continued to pull in other downed Pegasus ponies. Curious, she got up and walked over to him.

“…Thanks for saving us…saving me. Who are you?” Spitfire asked.

“Names Thunderwing, ma’am.” Thunderwing said.

Fleetfoot was thankful as well and assisted him in bringing the Pegasus recruits to safety. Immediately, they remember Soarin was on the ground and called to him. Thunderwing turned.

“Let me distract the alicorn and move him away from Soarin, while you retrieve him.” He said.

Both Spitfire and Fleetfoot looked at him, focusing on a way to pull the alicorn away. Suddenly, he flew toward Khaoios and sideswiped his face. Now that he was distracted, Spitfire and Fleetfoot moved in and dragged their partner off the field. Khaoios turned.

“You!” he snared.

“Bingo!” he said, flying as fast as he could.

Disappearing from Khaoios sight, Thunderwing flew back to the other Pegasus ponies. Landing nearby Spitfire and Fleetfoot, they aided Soarin only to see him struggling to his hooves.

“Ugh…what happened?” He asked.

“The alicorn hit you.” Fleetfoot said.

“At least you’re alright, thanks to this Pegasus’ bravery.” Spitfire commented.

Thunderwing smiled. Suddenly, another squad of pegasus ponies appeared and tried to hold off Khaoios, yet they too could not defeat the alicorn. As explosions continued, a pegasus stood on top of a building. When the light of the moon was covered by the clouds, General StoneColt appeared.

“Picking on ponies again, you worthless piece of gutter trash?” StoneColt insulted Khaoios.
Khaoios growled.

“You!” he said prowling towards him.

Serving as a distraction, Fluttershy, Rainbow Dash and the other pegasus ponies arrived at the academy. Trying to ready position, glass shattered onto the ground, making Khaoios turn realizing he was once again distracted. Yet, StoneColt noticed, he was merely faking his distractions. As he unleashed his magic, Twilight and the Archivist appeared, using their magic to merge into one, only hitting Khaoios on his broadside.

“You AGAIN!” he said.

Immediately, Khaoios returned fire blasting a water tower. It crashed down landing on Princess Twilight and the Archivist. Totally unexpected, StoneColt called out to all ponies to take cover. As the ponies took cover avoiding the attack, they all fought bravely to defend the academy from the alicorn. Now that everything was a mess, Voyager turned.

“What now, General?” he asked.

StoneColt couldn’t analyze the situation. He could only feel surprised by Khaoios sudden return and thus realized he has become much more powerful than before, depending on both quick thinking and full force.

As for Moonraker, trying to be a hero charged at Khaoios.

Rainbow Dash called to him, but as she did, he got knocked away by Khaoios’ wing.

“Pathetic, little pony. Trying to be a hero.” Khaoios said.

StoneColt and New Horizon called to Moonraker, but it was no good. Trying to save their brother, Twilight broke out of the wreckage and tried to fly towards him, but her wings made her immobile.

“Say good bye to your…” Khaoios was interrupted after being hit by a powerful beam, sending him into a building, landing on his back.

Suddenly a white alicorn slammed onto the ground, standing on top of Moonraker. Amazed by its power, the pegasi could not get a glimpse of it, until the moon shined on the alicorn. Khaoios got up and looked at his opponent. Twilight’s eyes suddenly widened.

“Is that…” she paused.

“…Paguseus.” StoneColt said proudly.

Ironwing Interstellar Paguseus arrived just in time, saving his son from Khaoios.

Chapter 7: Strategize

“Father…” Moonraker called out.

“How many times have I told you to stop being a show off, my son.” He spoke.

“Well…uhh…” Moonraker paused.

“You can do better than that.” Paguseus said.

He walked forward towards Khaoios.

“You!” Khaoios’ eyes glowed.

“You! Yes! What are you doing here! I thought I locked you up?” Paguseus spoke back.

“I broke free from that Astronomical Prison of yours, and now I shall return the favor, sending you into your own prison.” Khaoios yelled in rage.

“Pfft…I’d love to see you try, Khaoios. However, I do not appreciate you picking on my children to get to me. And you know that well.” Paguseus spoke.

Khaoios, enraged by his words charged at him, but within a blink of an eye, he disappeared only to appear behind Khaoios. Twilight, Rainbow Dash, StoneColt, and the other Pegasus ponies were in awe, seeing how fast Paguseus was. His reflexes were so quick, the Wonderbolts were speechless.

“Welcome back, Marshall.” StoneColt smirked.

Suddenly, a fight ensued between Paguseus and Khaoios attacking a dodging each other’s attacks, only to crash into a building. While the battle continued, Applejack, Rarity, Pinkie Pie, and Amethyst Crystal arrived. By immediate surprise, Amethyst ran towards the two alicorns. The Archivist quickly ran to her.

“No, Amethyst!” the Archivist called out.

Paguseus turned, thinking some pony was near was kicked in the face and slammed to the ground, with Khaoios stepping on his face.

“Behold…I have finally put you down, my foe.” Khaoios boasted.

The Archivist managed to catch up to Amethyst and tried to hold her back. Insisting her to not get involved, she tried to fight back.

“NO! FATHER!” she cried out.

Khaoios turned.

“…Amethyst?” he whispered.

Now distracted, Paguseus threw himself back on his hooves, sending Khaoios into another building. At that moment, he sensed something unusual of his foe. He turned and saw the Archivist holding back Khaoios’ daughter, which surprised him deeply. Knowing that she is the only pony that could reason with him, tried to stop Khaoios. Unfortunately, he was then kicked back by Khaoios, taking flight and fleeing the Wonderbolts Academy. Amethyst and the other ponies watched as Khaoios flew away. Upset that her father left her, Amethyst began to cry, feeling abandoned. The Archivist put her hoof around her, trying to comfort the young pony.

“So that’s his weakness, but an unusual one. It’s more like a key to stopping him completely”. Paguseus thought to himself.

StoneColt flew beside his master.

“Nice to see you back, Marshall.”

“Indeed. Status Report?” Paguseus asked.

“Some buildings need some rework. As for the ponies, quite a few injuries, but they’ll live.” StoneColt replied.

“Understood. Have those who are at full strength to tend to the injured. I have to speak with the Archivist.” Paguseus responded.

“Yes, my master.” StoneColt said heading back to the main building.

Paguseus walked up to the Archivist, with the Mane Six and Amethyst stood. Rainbow Dash was in awe by his strength and tried to speak, but was blocked by Fluttershy. Twilight stepped forward.

“Greetings, Master Ironwing Interstellar Paguseus. I am…” she bowed her head then was soon interrupted.

“Yes…I know who you are. Twilight Sparkle, Princess of Friendship and of course your friends. Guardians of Harmony I should say.” Paguseus spoke.

“Guardians…of…Harmony?” Rarity tilted her head.

Rainbow Dash flew up to him.

“Whoa, Master…uh…Ironwing. Your so fast and that speed…whoosh…you end up right behind Khaoios was…ah!” she said excitedly.

Paguseus scoffed.

“Oh…I gotta race you, please…” Rainbow Dash pleaded.

Hearing her words, the Archivist and StoneColt face-hoofed themselves.

“Oh no…she didn’t.” StoneColt said, closing his eyes.

Paguseus chuckled.

“As much as I would enjoy a race, I must respectfully decline. My speed would hurt you because since I travel at extreme speeds, I give off a screeching sound that can disable your flight pattern. That’s why I limit my speed when I am on planet. Up in space, I travel at my fastest speed. However, I admire your spirit when it comes to your loyalty. Not to mention, performing a Sonic Rainboom is quite rare. Well done.” he replied.

Rainbow Dash felt disappointed for a moment, but at the same time she felt proud by Paguseus’ words. The Archivist stepped in, with Amethyst at her side. Very unusual to see the offspring of Khaoios, surprise Paguseus deeply.

“May I ask you something, Madame Archivist? Why is Khaoios daughter here?” he asked.

The Archivist turned.

“She came to see me, because after Khaoios reappearance three months ago, she tried to find the general to get to you. Then when she heard her father was defeated and Xenxus reappearing, she went out to find you again. That is…when she found me just this recent.” she replied.

Paguseus turned to Amethyst.

“My dear, why were you trying to visit me?” he asked.

Amethyst lowered her head, afraid to answer him. She could only think the worst and that her father would be imprisoned again. Paguseus, sensing her feelings, sat down. He exhaled.

“Let me tell you something, and not as a foe but from the words of a father. What Khaoios is doing; he is doing for you. However, when we first encountered him, the Queen saw him as a worthy alicorn because of his intelligence. One major thing I respect about your father. The one thing we are disappointed with, is his actions. It proved to be harmful and thus why I was ordered to lock him in the Astronomical Prison. Now, with his recent actions, he cannot be allowed to perform this type of catastrophe again. Especially the nerve to harm my children.” Paguseus explained.

“But my father is good. He has always been caring and I…I don’t know what to do. I called out to him and stared at me, thinking I was just a mere foal. And…he flew away…leaving me…” Amethyst teared up.

Twilight and Applejack shed a tear, feeling her pain. They walked over and tried to comfort her the best they could, but still she felt extremely hurt. Suddenly, Twilight realized, Amethyst wasn’t blaming herself, she was blaming Khaoios. Paguseus explanation made her understand the truth behind her father. A truth that was never meant to be told.

“I know how much you love your father. Believe me, and my children know who I am referring to. I had another daughter that disappeared from me years ago. Yet, I remember her…but she doesn’t remember me, and the one thing I remember that I can only blame myself on is not being there for her. In this case, you are upset because your father is driven to make the world a better place for you, but is not physically there for you.” Paguseus concluded.

Suddenly, behind them, Paguseus six children arrived with General StoneColt.

“Father. Everypony is fully healed. What are your orders?” Mariner asked.

Paguseus turned and observed the ponies around him, then stood up. He looked East, to the rising Sun. Thinking for a moment he looked down.

“General, I need you along with The Archivist, Amethyst, the Princess, and her friends to investigate this recent issue. Mariner, I want you, Orbiter, and Deep Impact to take a Wonderbolts squadron and scour Equestria alerting cities, town, warning about the alicorn. Do not mention Khaoios’ name, or else there will be a major panic. Moonraker and New Horizon I need you to continue to tend to the injured here. Voyager, you’ll be going with the General to assist. Do you all understand?” Paguseus ordered.

“Yes, Sir.” They all replied.

“But, Master Paguseus...What about Khaoios?” Fluttershy asked.

“I will being paying a visit to someone of importance first. Then I will follow him. At this point, I doubt he’ll be attacking any cities.” Paguseus said, taking flight and leaving the Academy.

“You heard the Marshall. Let’s get to it.” General StoneColt yelled out.

Chapter 8: The Secret Library

Immediately, everypony went to begin their duties. StoneColt walked into an office and sat at his desk. The Archivist, Twilight and the other ponies stood in the room. Behind, Thunderwing passed by, assisting Spitfire, Fleetfoot, and Soarin.

“Thunderwing, would you mind shutting the door please?” StoneColt called out.

“Yes, General.” Thunderwing said, closing the door.

The ponies looked at one another quietly.

“You have something on your mind, don’t you?” The Archivist said.

“Yes, I do. And I have a feeling that he’s gonna plan out his next move. A move we cannot intercept.”

Twilight stepped forward.

“If I’m not mistaken, Khaoios can’t plan his next move. Without the Artifact, he’s weak. Wait…where is the Artifact?” she said.

The Archivist’s eyes widened.

“I know what you’re gonna say, Archivist but I doubt very much Khaoios would be that stupid to steal the Artifact.” StoneColt said.

“No, it’s not that. Twilight may be on to something. Khaoios can’t form a strategy without the Artifact, however he has something else of value.”

“His Library…” StoneColt exhaled.

“Exactly.” The Archivist grinned.

“A Library. Hey, that’s up your alley, Twilight.” Applejack exclaimed.

“Now…uh…where is this library?” she replied, nervously.

The ponies looked silently at one another. The Archivist and the General however, shook their heads for they knew where the library was. Unfortunately, they could only determine that it was destroyed thousands of years ago because of the downfall of the Bronco-Titans. Twilight became quite curious.

“If I may ask, Madame Archivist. What and where exactly Khaoios’ library is?” she asked.

“Well, since we already know Khaoios is the Master of Intelligence, he commonly used his Artifact for strategies, but he remained in his library when planning out his next moves.” The Archivist responded.

“…and before you ask. There are three…yes, three Libraries of his.” She continued

“Not to mention, he has an extraordinary diamond collection in his trophy room” StoneColt added.

Rarity ran up and slammed her hooves on the desk.

“Did you say...DIAMONDS??” she asked.

“Yes. Khaoios collects diamonds to study its infrastructure so that he can create crystals with the glare of a diamond.” StoneColt mentioned.

“That’s because how much they glare and serving as a beacon for him.” He continued.

Rarity fainted.

“Oh boy.” Applejack shook her head.

“Now, with regards to the library, where are they?” Twilight asked.

“From what we know, they were all destroyed, but I’m getting to the point that there is another. His main library that we all thought was long destroyed.” StoneColt stated.

The Archivist turned. She could not think of it, but then it hit her that Khaoios had one specific library, containing almost all of his studies. She looked around for a map of Equestria until Pinkie Pie hopped over with it.

“I got it.” She said, laying the map on the desk.

Opening it up, they looked at the areas of interest, but could only deny each one, excluding one area, that caught the Archivist’s attention and even stated it wasn’t on the map. It was kept hidden from the kingdom. The Mane Six looked at one another, only to stare at StoneColt’s face. Yet, before he could answer, a knock was heard on the door.

“Come in.” StoneColt said.

Opening the door, Mariner stood.

“General, we’re about to depart. Any recommendations besides alerting the populated areas?” he asked.

“Not at this moment. Proceed with caution and good luck.” StoneColt replied, as Mariner closed the door and left.

Continuing to observe the map, Amethyst walked up to them.

“What about the temple? When I was a foal, I remember seeing a large library and unusual objects that I could not even describe. Yet, it was isolated on an island over to the East.” She said.

They all looked at her and StoneColt then realized a small chunk of land, South East from Manehattan. He slammed his hoof on it.

“What is it? What temple was she referring to?” Rainbow Dash asked.

“Father’s old temple. The planetarium. It was destroyed when he encountered Xenxus during the war and due to its heavy damage, he abandoned it.” Voyager commented.

The Archivist took a while to absorb the information until StoneColt exhaled.

“The Planetarium Temple was converted into the Ancient Library, which was supposedly lost. I thought the island had exploded.” StoneColt said, turning his head to the Archivist.

“What? How?” The Mane Six asked.

“The island was a mountain, but then we realized as we got closer that it was a massive volcanic.” The Archivist said, staring at StoneColt’s face.

“Krokatani…” he said.

Deep within a forest, Khaoios rested his wounds but could not rest what was important to him. Feeling upset that his daughter saw what he truly was, hurt him emotionally, and believing that he failed her as a father. However, driven with rage from his previous defeat, he flew to San Palamino Desert in search for one thing…the Artifact. Sensing its presence, he used his magic to pull it from the ground, knowing it was concealed in the temple thousands of feet below his hooves. Within minutes, the Artifact reappeared before him, as it continued to burn continuously. Before turning away a light appeared behind him.

“Khaoios…don’t do this.” The calm voice spoke.

Khaoios turned and noticed an illusion of the Queen appeared.

“You cannot stop me, you majesty. I’m only taking what belongs to me. Nothing else.” Khaoios spoke back.

The Queen shed a tear for a moment, sensing his pain.

“I know you are only doing this for you daughter. Believe me, I’ve done the same thing to my two daughters, but sometimes they need to learn how to experience things on their own.” She said.

Khaoios exhaled.

“I deeply understand. However, mine is still young and her mother wasn’t there for her and I shall make up to it. And you know that…your guardians, including my second brother is in the same position. Don’t lecture me about what I must and mustn’t do.” Khaoios replied.

The Queen shook her head.

“There is always another way Khaoios…” she whispered as the illusion disappeared.

Khaoios soon flew away from the scorching hot desert to an unknown location. At that moment, he looked back at the deserts emptiness and thought about the Queen’s recent words. He knew exactly that as the intelligent one, there are always ways out of current situations. Safe ones, he thought, but all he could think about is making sure his daughter is safe to whatever it costs. Even if that means it costs him his life. Silently, he disappeared high within the clouds.

Chapter 9: Mystery of the Element of Space

Nightfall approached, as Twilight, StoneColt, The Archivist, and the other ponies made it to the south eastern part of Equestria. Strangely, they encountered stormy weather that slowed their advance, forcing them to take shelter within a cave. StoneColt looked out at the stormy weather and could only stare. Rainbow Dash flew up to him.

“Probably some pegasi ponies added pushed the clouds here to have a stormy condition. I could probably move it away from us.”

“This isn’t the work of Pegasi. This is a natural storm originating from the Triangle. Hurricane weather, to be specific.” StoneColt said.

“How is that possible? We all thought the Everfree Forest is the only area on Equestria that has everything move on its own.” Fluttershy said.

“Not everything. Weather that originates from the oceans are natural. In this case, we are in an area where it’s referred to as the Triangle because it is an area of secrets. Most disappearances occur there and to this day, it remains unsolved.” StoneColt commented.

Twilight turned to the Archivist.

“Could it be possible that this…Volcano Island of Krokatani may reside in there?” she asked.

“Krokatani is only a legend, so I doubt very much he would go to a place where it’s commonly known to be just a fictitious island, spoken by its surrounding tribes.” The Archivist responded.

“Do not underestimate Khaoios’ intelligence, Madame Archivist. I think what Twilight said can be a major possibility. Not to mention, since it’s an area of disappearances, it wouldn’t surprise me that the reason for the disappearances is to keep intruders away. Yet the question is…from what. Why would Khaoios keep intruders away?” StoneColt said.

The ponies were all but silent for the moment. Brainstorming on what StoneColt said made them all curious. What was Khaoios hiding and why is it so important. The only way to find out, Twilight thought…was to physically go there. A perilous journey soon awaited them, but rest was highly needed as the storm continued throughout the early evening. Twilight remained awake, still thinking about the mysterious Triangle and its connection with Khaoios. She looked over to see StoneColt still observing and thinking. She walked over to him.

“I see you can’t sleep either, General.” Twilight said.

“Yes. It appears so.” StoneColt replied.

“I heard what you did to Xenxus, using Timaeus’ Element of Time. Shame that it turned you to stone, to be honest.” He continued.

“Yeah. That was pretty bad, from what I heard. Yet, I was curious. Since the Element of Time was discovered and used by me, and proved to be a weakness to Xenxus with the combination of our Rainbow Powers; what is Khaoios’ weakness. Last time we fought him, our Rainbow Powers failed, twice. Is the Element of Time the only thing that can stop him?” Twilight said.

“No. The Element of Time is useless against Khaoios. However, I wanted to ask you.” StoneColt paused.

Twilight looked at him.

“How much do you know about the Element of Space?” StoneColt asked.

Twilight nodded her head.

“I see. You have a lot of learning to do, young Princess as both Paguseus and Khaoios would say.” StoneColt scoffed.

“What is the Element of Space? What is different from this one from the Element of Time?” Twilight asked.

“Well, the Element of Space was created by my master, Paguseus. Its power grants the user the knowledge of understanding what’s outside this world astronomically. For that matter, things that we don’t know in terms of astronomy, the Element does. Yet, I am sure that this element also has its own side effect as did the Element of Time’s fossilization-stone spell.” StoneColt spoke.

“There’s another side effect to this one?” Twilight twitched.

“Oh yeah. And that was first experienced with Paguseus youngest daughter. That’s why he said before to Amethyst that when his daughter used it, she disappeared. The problem was that when she disappeared, the Element remained nearby by she wasn’t. It was as if she was taken to a different planet or an alternative world, which could also be the reason why Alteros was fuming over Paguseus. Oh boy do I remember laughing that entire time.” StoneColt laughed.

“Wasn’t funny during that time, General. Remember that she may have used both elements which combined its power to make herself disappear.” The Archivist said walking towards them.

“See you can’t sleep either?” Twilight said.

“Appears to be. However, the Element of Space, in basic terms is that one who wields it and is seen unworthy, the Element will banish you off planet. Yes, off planet to a point of no return. Most common place it will banish you to is the Astronomical Prison. Why? Simple? It’s like stealing something and then going to jail for it. Same as the Element. You steal the Element, it sends you directly to jail…only this jail is filled with ruthless enemies. Enemies far worse that Tirek, himself.” The Archivist added.

Twilight gulped, in a sign that she was deeply nervous. She knew that she would not want to go through a similar incident as she did with the Element of Time, nor a place where she would get banished into a dark and oblivious area.
“Where is this Element now?” Twilight asked.
Both StoneColt and the Archivist looked at one another, and nodded their heads. For once, they had no idea where the Element is. Slowly becoming drowsy, she decided to go to sleep beside her friends. As she slept, the Archivist felt worried as she looked out into the stormy night.

“I was right this whole time.” She said.

StoneColt tilted his head.

“Come again?” he asked.

“I was right about this matter getting worse. Seems this entire plan was orchestrated to a point in time where no pony knows about it, and for that matter disturb the peace. They’ve been like this for centuries and now, it seems they are truly feeling the “kick” of what we felt years ago.” The Archivist commented.

“Well as the master would say, don’t let dark thoughts cloud your judgement. Keep them clear so you can continue on with your life. Learn when to let go.” StoneColt finished.

He walked over to a flat slate and soon fell asleep followed by the Archivist, both waiting for the storm to pass.

Chapter 10: "Most Islands Hold Deadly Secrets"

As the storm continued, Paguseus arrived at the bottom of Mt. Tse’Reve, glazing up at the cold and snowy Voltday Pass. Due to its poor weather condition, Paguseus' visibility will be critical, thus making it harder to locate the abandoned temple up buried high above the mountain. Climbing his way to the top, he noticed distorted orbs, floating around like bubbles at the top of the mountain, indicating he was near the entrance. Finally arriving at the broken gate, he safely made his way inside, hearing water drops echoed throughout the dark temple, laying only ruins from a long battle dating back before Equestria. He stopped for a moment, observing another distortion orb in the air. He knew he was getting closer to that specific “someone”. Finally making it through the doorway, Paguseus squinted for he saw a pony within the temple.

“Janus…I need to speak with you, now.” Paguseus called out.

From the shadow, Janus appeared into the light. He had gray fur and had a mane resembling a warrior. He had been residing in the Temple to prevent ponies from passing through the temple. Knowing the temple was a “gateway” to different worlds, Paguseus sensed something was wrong.

“Yes. Master Paguseus. What can I do for you?” Janus asked.

“I wanted to ask you something. Mt. Krokatani and the Triangle. What is it?” Paguseus questioned.

“Mt. Krokatani and the Triangle, you say? What makes you so curious about that?” Janus asked.

“On my way here, my apprentice informed me that the south east area of Equestria was covered with catastrophic storm conditions. When he had told me that disappearances had occurred in the area, I began to question that. That’s why I came to you. I thought you would know something.”

Janus rubbed his back neck and exhaled.

“Krokatani is a powerful volcanic island that supposedly exploded, however when I viewed it from the mirrors…it not only exploded, but disappeared." he commented.

“Disappeared? How does an entire island just disappear?” Paguseus asked.

“That’s the thing. This world is filled with such mysteries that I cannot even solve. Yet, when the island disappeared, I sensed it on this planet, but didn’t know where.” replied Janus.

“So it teleported onto this planet and neither of us could sense it. Only reports of disappearances.” Paguseus added.

“Yes. Its importance, I have to admit is unknown to me. What connection between Khaoios and Krokatani have, I don’t know. All I could sense is whatever is in there, Khaoios wants badly.” Janus continued.

Paguseus paused for a moment.

"Remember, Master. Most islands hold deadly secrets." Janus added.

“I see. Is that all?” Paguseus asked.

“Yes. Yet, I’m surprised you came to ask me? Why, if I may ask?” Janus asked.

“Well, we have not seen Alteros for a thousand years and without him, we have difficulty solving certain problems. In this case, Khaoios reappear and the concealed area in the eastern seaboard. If he were around, he would’ve answered them, but I decided to see the gatekeeper; which was you, of course.” Paguseus stated.

“I see what you mean.” Janus replied.

“By the way, what was the name of the island when you first saw it?” Paguseus asked, before leaving.

Janus looked up at Paguseus.

“The species in that world called it…Krakatoa.” He replied.

“Krakatoa, eh. Very well. Thank you for the information. I shall relay the message to my apprentice.” Paguseus replied, flying out of the temple.

Janus sighed.

“What did Paguseus want?” a shadowy figure stood nearby.

Janus suddenly shape-shifted into his original form and by surprise, it was one of the Bronco-Titans apprentice, Palomede the traitorous pony.

“Nothing, sir. He only got what I have provided him with. What shall I inform Master Khaoios with?” Palomede asked.

“Do not worry. My brother knows exactly what he did. Let’s see how well they can escape the island.” The shadowy figure smiled.

"But, master...the island. It possesses a lot of secrets that we need. Destroying it will destroy our own plans?" Palomede said.

"Khaoios already stripped the secrets from Krokatani. Yet, one thing we cannot remove is the island's power source." the shadowy figure continued.

"Power source?" Palomede asked.

"Yes. The Power Source controlled by the relic that was created by its Master of Space." the shadowy figure concluded.

Palomede tried to think about what his master meant until he realized what it was. He looked up to him and grinned sinisterly.

“Understood…my master.” he replied.

Morning came on Equestria as Twilight and company continued their routes to Mt Krokatani only to spot a boat, ready to set sail. It confused them for a moment as if something knew they were coming, but who. Curious, StoneColt headed down to the dock to investigate, and called for Voyager to assist. Amethyst stood nearby until suddenly, her body glowed. Shooting a beam from her body served as a beacon. How and why, they continued to feel puzzled. Suddenly, she began to speak in an unknown language, then immediately the Archivist looked up in shock.

“She’s speaking Brogsentarian. Khaoios’ language.” She said.

“Brogs…what now?” Applejack and Rainbow Dash asked.

“It’s an ancient language spoken by the ancient ponies of the North.” Twilight said.

After a minute or so, Amethyst dropped to the ground, not remembering a single thing that occurred to her. Suddenly, StoneColt called out for the storm strangely subsided and cleared away revealing something extraordinary. Though the stormy clouds stood above calmly, the island revealed itself. The ponies all glazed at the island.

“Mt. Krokatani. Now to uncover what’s inside.” The Archivist mentioned.

“Looks scary and dangerous.” Fluttershy responded nervously.

“Oh come. Lalalalala” Pinkie Pie hopped over to the boat.

“Come on, girls.” Twilight said, following behind Pinkie Pie.

On the way down, Mariner, his brothers and the Wonderbolts arrived.

“General! You’re here?” Mariner called out.

StoneColt and the other ponies turned.

“Mariner? What are you doing here?” he called out in reply.

Mariner flew down to them. Exchanging conversations about their travels, he informed them to meet at the beach side near the volcanic island. Surprisingly, StoneColt never ordered them to arrive there, but decided to let it go. He immediately thought if something were to happen, at least they would remain on the beach keeping an eye out for the Bronco-Titan. Remaining behind, Amethyst stood by Mariner’s side.

“Are you feeling alright, Amethyst?” Mariner asked shyly.

Amethyst began to blush unexpectedly.

“Yes. I am fine, Mariner”, she softly replied.

Chapter 11: The Island of Mt Krokatani

Finally setting sail, they sailed to the island that stood silent, but spooky. Twilight could only sense trouble nearby. After several minutes, they reached the island, ten miles away from the mainland. Slowly the group made it through an unusual looking gate, until it opened by itself revealing something that was beyond their understanding. Within the volcano that looked short, at the top, revealed to have a massive abandoned temple in the structure of a castle. Observing the castle, they noticed objects that they could not identify. Something beyond their technology. StoneColt continued to look around and slowly walked down to the structure. Twilight noticing how massive it was, became astonished.

“This place…it is…” Twilight paused.

Crossing over a bridge, the doorway opened to a massive hallway filled with orbs. Each one looked like bubbles that had Pinkie Pie quite excited. Hopping around and popping them, the Archivist tried to determine what they were. Rainbow Dash bumped into on orb that popped, creating a shockwave knocking her onto the ground.

“Rainbow Dash! Are you okay?” Fluttershy called out.

“Yeah…I feel…ugh” Rainbow Dash fainted.

“Madame Archivist. Come in here quickly!” StoneColt yelled out.

The Archivist, Twilight, and the other ponies ran into the room to be in complete shock. The entire room, was a massive library, with technology beyond their own. Each one went down an aisle looking at the books. Twilight happen to come across another room, with a giant telescope. As she walked closer, a red beam began to blink as she passed through it. Distracted, she turned and noticed something of deep importance within the room. Passed the telescope was a pyramid like structure with an object standing above it. While the other ponies continued their search through the library, Twilight walked slowly to the pyramid climbing up one step at a time, thinking each step contained a trap. In the library the Archivist blew away any dust from the books and read through them. Some of the books had unknown manuscripts she had never seen before. Even scientific formulas that she could not interpret. It was as if the library was hidden with secrets that neither her, her associates, nor her master knew about. StoneColt, continuing his reconnaissance throughout the castle, came across another room, only this time, he heard cries for help. Quickly barging down the down, he noticed there was a pony resting in the back of the room. Not even thinking he ran to the pony and called out to the others.

“Don’t worry. You’re going to be okay.” StoneColt said.

The pony muttered words that he could not understand. Soon, the Archivist ran in and by surprise, she recognized the pony. StoneColt turned and cleared away the pony’s face, revealing to be Janus. The Archivist crashed to the ground and quickly called to the other ponies to bring water. Rarity immediately found water from the fountain and ran over with it. Giving it to the Archivist, Janus drank the entire bowl and insisted on having more. Applejack, Pinkie Pie, hurried over, while Fluttershy stood by the doorway with Rainbow Dash, still dizzy from before. As the Archivist tried to speak with Janus, Twilight continued her way up to the pyramid, only to see, it was the Element of Space. However, it surprised her that it was there and no pony knew about it, not even the Archivist nor the General. In the room, Janus picked up his head.

“Khaoios…” he muttered.

“Khaoios? What did Khaoios do?” The Archivist pleaded.

“He…its” he paused, trying to catch his breath.
“He what? It’s a what?” StoneColt said.

“It’s…a…trap…” Janus muttered again.

Immediately, the Archivist turned.

“Where’s Twilight!” she asked.

The ponies looked around and lost sight of her. Quickly, she told them to assist the general, while she goes back for Twilight.

“Twilight!” the Archivist called out.

Twilight was in complete hypnosis as she took the Element. The Archivist then barged through the doorway.

“NO! DON’T TOUCH THE ELEMENT!” she screamed out.

Suddenly, as Twilight removed the Element of Space from its spot, an explosion rocked the entire castle, knocking everypony off their hooves. As the explosions then continued, the Archivist yelled to Twilight for her to jump. Luckily, she jumped just in time, before the platform she stood on exploded in a ball of fire. Catching her, the ceiling began to crack and fall down onto them only to dodge them safely. StoneColt carried Janus on his back and hurried with the ponies as fast as they can out of the castle. Regrouping, the Archivist looked at StoneColt.

“We gotta get out now!” The Archivist said.

“How did I not see this coming?” StoneColt commented.

Twilight, still with the Element in hoof, surprised the both of them. They didn’t even have the words to describe on how she found it and got it. However, something else troubled them, only to realize one thing. Khaoios orchestrated the entire operation, he wanted them to go into the castle and go down with it. Finally, making it outside, explosions continued to rock, until lava shot out from the bottom. The volcanic island was about to erupt. Across the way, Mariner and the other ponies watched as the island shot up lava and exploded. Rocks tumbled from the top, slamming into the structure and destroying information that has not been decrypted. All that worthy information would soon be lost forever. Twilight looked back at the crumbling castle as the explosions then destroyed the gate, behind them and destroy the bridge. As the bridge fell, they all followed but were saved biting each other’s tail, climbing up. Climbing as fast as they could, they safely made it up and through the cave reaching the dock.

“Hurry! Set sail and let’s get the hay outta here. STAT!” StoneColt yelled out.

The ponies hurried and set sail, leaving the island as the mountain continued to explode. From a distance, one Wonderbolt member called out that they had spotted the General. Awaiting them at the shoreline, lava began to break through the mountain, causing waves to rise up, pushing them away from the island. Pinkie Pie stood on the side of the boat, sea sick from the waves.

“Uh…Pinkie? You okay?” Applejack asked.

“No…” Pinkie covered her mouth.

Further and further from the island, the ponies turned as the volcano finally erupted, exploding so big, it destroyed the island, by slowly sinking into the dark and watery abyss. Reaching the island, the ponies threw themselves on to the sand, trying to catch their breath. The Archivist and StoneColt walked over. The General, carrying Janus walked slowly to the top of the hill. Passing by, Mariner walked to the Archivist.

“What happened?” he asked.

“The castle was concealed with information I could not even describe to you that went up in flames.” The Archivist spoke distraught.

“Translation please?” Orbiter said.

“Khaoios rigged the place. He knew we were coming, but we didn’t realize it, until Twilight found your father’s relic.” StoneColt replied.

“…and I see Janus as well.” Deep Impact added.

“Oh yeah.” StoneColt replied.

Chapter 12: Confrontation

Safely off the island, StoneColt and the Archivist sensed a presence communicating with them.

“I need the two of you to go up to Manehattan, now! Khaoios has taken the city hostage again.” Paguseus spoke telepathically.

“We have the Element of Space, Master. And…another associate. Janus!” StoneColt thought.

Paguseus, who was flying over the skies of Equestria at the moment jumped in shock.

“Impossible. I saw Janus at Mt Tse’Reve…unless…never mind. Head to the city. I’ll meet you all there. One last thing though, Twilight’s little dragon…he’s no longer little. Proceed with extreme caution. Do you understand me?” Paguseus concluded.

Both the Archivist and StoneColt exhaled, fearing for the worst.

“Yes, sir.” They both thought and turned to the ponies.

“The Marshal has confirmed that the city of Manehattan has been capture by Khaoios again. And sadly he’s not alone on this one.” StoneColt announced.

“Who’s with him?” Twilight asked.

Both the Archivist and StoneColt remained silent.

“We don’t know at this moment. Our first priority now is to head for the city.” StoneColt said, taking flight.

Mariner called upon the Wonderbolts to follow behind. Flying like a flock of birds, they all hurried to Manehattan. The Archivist turned and continued to glaze at the island as it slowly sunk, before it disappeared. The Archivist called out to her, and Twilight turned. She tilted her head in confusion, wondering what Twilight was thinking. Instead, she followed the Wonderbolts up to the city.

At Manehattan, ponies took to the streets as Khaoios flew over them, holding his Artifact. Landing on a tower, he observed the area from when he was last there and noticed many changes were added, preventing him from perform any strategy. Noticing ponies were running across the bridge, he turned and roared out from a distance. Hearing it, the ponies stopped one the ground of the bridge shook. Within the mist a large, reptilian like creature stomped towards them. As it, cleared Khaoios grinned.

“Meet my slave, wretches.” He spoke.

The ponies looked up and noticed it was a fierce some dragon, with green spikes and light purple scales. Roaring out, the ponies were pushed back into the city, thus trapping them, exactly what Khaoios had planned. While Khaoios continued to hold the city hostage, nothing would prepare Twilight for what was awaiting her. Especially someone close to her, who was now…her bloodthirsty enemy. Hurrying and hurrying as fast as they could, Paguseus arrived at Manehattan flying overhead and observing the situation. Unlike his counterpart, he plans strategies fast without knowing the danger that could occur but instead maneuver them if he ever encounters them. He closed his eyes and began to calling out for his two other children back at the Academy.

“New Horizon. Moonraker. I need you at Manehattan, now. I along with your siblings will be waiting there. Hurry.” He spoke telepathically.

New Horizon and Moonraker picked up their heads.

“Yes, father.” They replied.

Flying to Manehattan, Khaoios walked along the skyscrapers, continuing to plan out new moves to obtain full control of the city. This time, knowledge of Equestria isn’t his primary goal, but conquering the city and moving slowly towards Canterlot. Paguseus recognized immediately what his counterpart was planning and slammed onto one of the towers. Khaoios turned with his eyes burning fire.

“You will not stop me this time, Paguseus.” He spoke.

“I cannot allow you to proceed any further, Master of Intelligence. I know your scheme as well as you know my quick-thinking. This fight is between you and I! Release these ponies and no harm shall be done.” Paguseus pleaded.

Khaoios grinned.

“Your compassion for these ponies is truly misplaced, Master of Space. I even have with me the Princess’ filthy reptile as my slave. Tell me, what advantage you have now, for your quick thinking will no longer be a problem.” He replied.

Paguseus knew from there Khaoios had possessed an ally, serving as a disadvantage to him. Having no other choice, a battle ensued between the Guardian and the Bronco-Titan, using their magic and zapping through buildings. Flying and flying with such agility, Paguseus soon began to feel exhausted. Strangely for a alicorn of tremendous speed would not be so easily tired was now losing his strength. Suddenly, the dragons tail hit Paguseus, sending him into a building, were he was knock temporarily unconscious. Roaring out, the ground began to shake to a point of cracking it, raising underground pipelines and train tracks. Fire hydrants burst, showering water all throughout the city. Manehattan was a war-zone.

As the base of a hill on the western side of Manehattan, the group arrived and noticed fire breaking out in the southern part of the island, fearing that Khaoios is now going fulling force. StoneColt stood upon a rock nearby and turned to the ponies.

“Alright, ponies. Our main objective is this. Luring Khaoios out of the city, however we must first separate him from his new ally, a dragon that we cannot identify.” He spoke.

“Dragon? What dragon?” Rarity asked.

StoneColt tried to hold his breath, preventing himself from revealing who the dragon really is. That is, until the creature roared out. Twilight not worried about any other dangers remained only focused on Khaoios. She walked up.

“For now, let’s not worry about the dragon. We had Fluttershy to take care of that…” she said.

“WHAT?” Fluttershy jumped.

She hid behind Applejack.

“Oh I can’t deal with another dragon. I just can’t.” Fluttershy said nervously.

“Oh come on, Fluttershy. You scared off one dragon, back at the Smokey Mountain. You can sure as hay can do the same with this one.” Rainbow Dash tried to encourage her.

The ponies looked at her. Fluttershy, still shaking in fear exhaled.

“Oh okay. I’ll do it for the safety of Manehattan.” Fluttershy proudly responded.

The ponies cheered. StoneColt turned to the Archivist and shook his head. The Archivist knew exactly what he meant, but decided to keep her head up high and go along with the situation. Rainbow Dash flew high and called upon all the Pegasus ponies to group up and lure out the dragon first. Then, Twilight will lure out Khaoios and take him out on the bridge. Strangely, what Rainbow Dash said was exactly what StoneColt was going to say and he grinned.

“Make the call, Dash.” He said proudly.

“Alright ponies. Let’s go!” Rainbow Dash called out, as the Pegasus ponies flew from behind. Twilight and the other hurried across the bridge and into the city. Sensing the ponies nearby, Khaoios slammed onto the end of the bridge confronting them.

“Well, ponies. What a surprise you managed to make it back to whence we first began. Intriguing.” Khaoios smirked.

Chapter 13: Nightshade Illusion

Amethyst tried to get in front, but the Archivist held her back Khaoios' immediately silenced himself once he saw her. His mouth and right eye twitched for he recognized something was terribly wrong. Now enraged, the Artifact unexpectedly responded to Khaoios' emotions, summoned a protective shield around the city, sealing them outside.

“Why would you seal yourself in the city, when we have your daughter?” StoneColt spoke.

Khaoios snorted.

“She can manage herself…Isn’t that right, my daughter?” Khaoios’ eyes widened.

Amethyst pushed away the Archivist and threw herself onto the ground. Trying to assist, they couldn’t help but realize Amethyst’s eyes glowed bright white. She was under the control of her own father. StoneColt turned towards Khaoios.

“You are a monster, Khaoios. The nerve to control the mind of your child! You’re mad!” he yelled out.

“This world is nothing but pain...sorrow…war…disgust. I shall be-rid of that.” Khaoios angrily responded..

He called for Amethyst, who was under his control to come to him. Not able to fight back, she walked to him, only to be confronted by Rainbow Dash.

“NO! YOU MUSTN’T!” she cried out.

Suddenly, Amethyst used her magic to throw Rainbow Dash on to the ground and continue walking until she stood beside him.

“Very good, my daughter. You have brought me something of value.” Khaoios said proudly.

Twilight nodded her head, feeling for Amethyst.

“Now, if you will excuse me, my daughter and I must catch up on a few things. In the meantime, enjoy your battle against your reptilian friend…” Khaoios turned away and disappeared.

“Reptilian…” Rarity paused.

“…Friend?” Twilight concluded.

Within an instant, The Archivist and StoneColt stood speechless, for they along with the other ponies confronted a dragon that looked too familiar to the ponies.

“SPIKE!” Rarity gasped.

Twilight felt a massive heartache at that moment. Khaoios took Spike, but only this time, he didn’t hold him hostage. He was controlling him, in his true form. Twilight turned to the Archivist.

“You knew…didn’t you?” Twilight cried.

The Archivist put her head down.

“DIDN’T YOU!” Twilight cried out in rage.

The Archivist shed a tear.

“Yes…We didn’t want you to confront Spike, for we feared that it would only distract you when defeating Khaoios…” she replied.

Twilight’s sadness soon turned to anger, causing rubble from around her to levitate. Her friends backed away, feeling the power.

“Twilight…” Fluttershy whispered.

“I…Will…NOT…LOSE…TO…KHAOIOS!!!” Twilight cried out, unleashing a powerful magic, breaking the shield.

Khaoios, surprised by the shield being destroyed turned and watched as Twilight took flight. Twilight turned to the ponies.

“Defeat Spike and hold him down. I will deal with the other animal.” Twilight growled out, charging to Khaoios.

The Archivist tried to follow her, but Spike blocked her pathway. StoneColt snared, knowing that this is exactly what Khaoios wanted. A solo fight between Twilight and him. StoneColt ordered Paguseus’ children and the Wonderbolt to circle around and distract Spike, luring him out of the city. Shortly thereafter, they proceeded to their duties, flying back and forth, hitting Spike all over his body. Twilight’s friends followed by luring him out of the city. With the path clear, the Archivist ran into the city.

“General! I’m going after Twilight. Hold Spike off here!” The Archivist called out.

StoneColt agreed and continued to assist the ponies on fighting the monstrous Spike. On the way up, Khaoios with the Artifact in his possession, observed the area, until he was surprised by Twilight, using her magic to hit Khaoios in the face. Twilight, burning with rage prowled towards him like a bloodthirsty wolf.

“I will make you pay, you demon. No matter what.” Twilight growled.

Observing her attitude, Khaoios right there and then, knew darkness was slowly consuming Twilight. He grinned towards her in intimidation.

“A strong dark power, I sense within you, Twilight Sparkle.” Khaoios said.

Twilight continued to prowl towards him, which Khaoios continued to sense dark magic surrounding her. She didn’t realize what power she was unleashing for rage was the only thing that came to her mind. All of a sudden, Twilight charged towards him, but was smacked away by the possessed Amethyst Crystal. Twilight, not hesitant on who it was retaliated with her magic, much more powerful than before. The Archivist who was racing towards the fight was unable to reach her. The power surrounding Twilight, created a boundary of disabling magic. Unable to take flight, she called to her. Hearing the Archivist calling to Twilight, Paguseus awoke from unconsciousness and struggled to his hooves. There he sensed darkness surrounding Twilight and without observing he hurried to her.

As the battle against Spike continued, another battle ensued between Twilight and the possessed Amethyst into a destructive battle. Jumping from skyscraper to skyscraper, the two unleashed magic, as powerful as the guardians and bronco-titans power combined. Khaoios watched as his daughter fought Twilight, but didn’t understand how powerful Twilight had become once something dear to hers was turned into her mortal enemy.

“How can this be? She’s just a mere princess pony. I feel…confusion.” Khaoios thought to himself.

Behind him, the Archivist arrived and walked slowly towards him.

“Look what you’ve done, Master of Intelligence. If you have not listened to the Queen, none of this would’ve occurred. Instead, you took your pain out on every pony including your daughter…” she paused.

“You know NOTHNG of my daughter, WITCH!” Khaoios replied angrily.

Suddenly Paguseus appeared, slamming on the rooftop.

“Yes, we do. She told us. She’s young and afraid…of YOU! Her own father, who thinks he can change the world for her when in fact it is he must change himself. How hard is that for you to not understand?” Paguseus yelled.

Khaoios’ rage grew.

“Do not lecture me, filth!” he spoke, charging at Paguseus.

Another battle ensued between Khaoios and Paguseus, with the Archivist hurrying towards Twilight. Calling out to her again, she stopped, only to be in shock by what she was seeing. An illusion of Twilight in the form of Nightmare Moon, but far worse. The Archivist backed away slowly, when Twilight turned towards her, revealing a distorted illusion of herself.

“…Nightshade…” The Archivist whispered.

Chapter 14: A Costly Victory

Down below, Spike was knocking the ponies away, one by one injuring them to a point of leaving them immobile. Rarity, struggled to her hooves and walked towards the monstrous Spike. Pleading and crying to him to stop, the monster raised his tail.

“If you want to put me out of your misery, do so. But I can no longer stand her and watch my best friend…my Spike-Wikey fall under control by some demon. Please Spike! Do it for us, do it for Twilight…DO IT FOR ME!!!” Rarity cried out.

Spike, hearing her voice halted and placed his tail down. StoneColt and the others watched as Spike bent over and confronted Rarity crying. Khaoios, sensing Spike’s feeling, threw Paguseus off and used the Artifact to regain control of him. With its power, it electrified Spike’s head, controlling him once again, until a blink of light from an unknown location, blinked reversing the effect and destroying the Artifact, completely. Khaoios yelled out in rage as his most valuable possession was destroyed in front of him. Spike and Amethyst regained their memories back and restored them to their original forms. Spike, not realizing he is high in the air, was caught by New Horizon.

“Don’t worry, Little Dragon. I’ve got you.” She said.

She landed and the ponies cheered, for the first part was completed and everything was returning back to normal. Yet, their celebration was short lived, for their next and final objective was to take down Khaoios once and for all. As they hurried, the Archivist noticed Twilight was beyond her control and that darkness was slowly consuming her. Luckily, she was not in a different form, the Archivist ran to her and embraced her from behind.

“That’s enough, Twilight! Please! It’s not worth it! Spike is safe.” The Archivist pleaded.

Twilight breathing heavily and eyes bright red, like a hungry wolf immediately awoke from this unknown power. Twilight fell to the ground, breathing fast.

“Wha…What happened to me?” Twilight asked.

Amethyst Crystal walked over to Twilight and put her head on her.

“I’m sorry, Twilight. I just couldn’t control myself nor you. We were both under some kind of mind control spell that exposed our dark side.” She cried.

Twilight smiled.

“Its okay, Amethyst.” She replied.

Though Amethyst told Twilight about what they both went through, the Archivist knew that only Amethyst Crystal was under mind control. Twilight wasn’t for it was a different and darker power within her. It frightened her that what she saw may be a vision of Twilight’s future if she does not control it. First thing that came to her mind was if Twilight were to continue such dark actions, she will suffer the same fate as Princess Luna did as Nightmare Moon. Knowing the danger, she remained quiet to keep Twilight on the bright side. Both Twilight and Amethyst turned to the Archivist.

“Let’s get Khaoios, shall we?” The Archivist spoke.

Both of them nodded in agreement.

Khaoios and Paguseus continued to fight, until finally Khaoios lost his footing, crashing on to the ground below. Now completely weakened, the ponies and even the residents of Manehattan walked over to see the downed Bronco-Titan. As Twilight, Amethyst, and the Archivist regrouped with them as well as Spike, Khaoios arose causing an earthquake as well as strong winds knocking away ponies. Paguseus, observing his mortal enemy sensed immediately danger.

“No! Khaoios! You will destroy yourself!” Paguseus called out.

Twilight turned.

“What’s going on?” she yelled out.

“His pulse….He’s going to unleash a pulse destroying himself along with everything!” the Archivist replied out loud.

“A Pulse? How are we supposed to stop it?” Applejack called out.

Suddenly, Twilight realized, she still had in possession the Element of Space. Quickly, she called to her friends to regroup and summon their Rainbow Powers. As they did, the ponies where in awe, watching the Mane Six group and use their magic with the assistance of the Element of Space against Khaoios. Khaoios watched as the Mane Six unleashed their magic, but failed in an instant. The power Khaoios was unleashing was causing the ponies to lose concentration. Paguseus grinned in disappointment.

“There’s not enough power!” he said.

StoneColt tried to crawl over but was lifted and slammed into a wall. The Archivist couldn’t move either. Looking and watching the other ponies try to go towards Khaoios, Amethyst made the most daring and ultimate decision. Using all her strength she ran to Twilight, knocked the Element of Space away and put it on her neck. The Archivist lifted her head and noticed Amethyst was now holding the element.

“NO! AMETHYST! DON’T DO THIS!!!”

Paguseus could not bear to see a young mare willing to sacrifice herself to save her father. The Archivist turned to Paguseus, insisting him to get her out. He looked back at Amethyst, shedding a tear. He didn’t have the heart to watch, but then she looked at him.

“Do it! I promise, it’ll be alright!” She yelled out to him.

Twilight and her friends sensed what they were about to do. Each one shedding a tear, they made the choice. Giving a final farewell, Amethyst smiled.

“Thank you…” she whispered.

In an instant, the Element of Space activated with the Rainbow Powers being unleashed, created a bright beam of light shooting high into the sky. After a few minutes, the city went into a complete blackout. Awakening after a minute, the ponies in the city celebrated. The enemy, Khaoios was once again defeated. However, nothing could cheer up the Mane Six, The Archivist, nor Paguseus. The decision Amethyst made to die with her father was heartbreaking to them. Twilight fell to her knees and cried. She couldn’t believe it, but knew that she did something that will haunt her for the rest of her life. Besides Twilight, her friends began to cry feeling her pain as if they were all connected and sensed the same exact thing. The Archivist walked over to StoneColt and put her head on him, crying.

“Why did she do it, General? Why?” she cried.

StoneColt, deep down sensed her pain. This is perhaps the first time, the Mane Six experienced a loss of an innocent pony they once thought of as an enemy and turned out to be a dear shy friend. Paguseus remained silent, then stood and walked away to the western docks. After a few minutes, the Mane Six, wiped away their tears and tried to think positive. Khaoios was defeated exactly what the attention was. Each one watched as the ponies of Manehattan cheered for them, and the Wonderbolts.

Chapter 15: A Father's Truth

As ponies from all over the city continued to celebrate, Twilight looked around for Paguseus, who was no where to be found. Suddenly, she spotted him near the docks, west of Manehattan watching the sunrise. She walked over to him and sat beside him only to have a long silence.

“I’m going to truly miss her, Master Interstellar. Are you?” Twilight teared up.

Paguseus exhaled and nodded his head.

"Do not worry, we'll see her again. I promise you." Paguseus replied.

Twilight’s tears cleared away.

"What do you mean?" Twilight asked curiously.

"I never said the Element of Space destroys the user if found unworthy banishes them. However, after Khaoios Overload Spell, I'm not sure." Paguseus replied.

Twilight's ears dropped. Paguseus cleared his throat.

“You know. As a father, this is the second time I feel this type of pain. After the loss of their mother, I vowed to give my life to protect them. Then as years went by, danger grew on us Guardians, leaving us with the ultimate decision by sending out children here where they can grow and learn on their own, receiving one quarter of our power. However, I had one that to this day I feel absolute guilt. and I only blame myself for not being there for her, thus becoming angry. She felt left out such as her being the only one of her siblings that couldn’t fly. She only wanted to be closer to her older siblings but failed to do so. Upset and angry, she disappeared from Equestria, making me feel a stronger sense of guilt. But then you came along. What she took from you was perhaps a sign not only to you, but to me. The friendship she couldn’t establish with her siblings…she did…with you. And I am proud to say, thank you for what you have done for her. Not only have you restored good in her, you’ve restored a part of my heart knowing that she can have a friend as nice and caring as you.” Paguseus spoke.

Twilight smiled, shedding a tear. Yet, something confused her. Before Paguseus took flight, Twilight picked up her head.

"There is a saying, Twilight Sparkle. Keep your friends close, but your enemies even closer. Sometimes, there's an enemy that will be considered an unsuspecting ally." Paguseus concluded.

Twilight smiled, yet was quite curious on what he meant. She looked uped to him as he opened his wings.

“Master? You mentioned to Amethyst one time that you had a daughter that disappeared. Who is that daughter you speak of?” Twilight asked.

Paguseus turned.

“The same one that took your crown…” he replied, before flying away into the Sunrise and disappeared.

Twilight tried to piece together his words until she finally realized who he meant. She looked up into the sky.

“Your daughter is…Sunset Shimmer…” she whispered.

StoneColt who happened to stand at the start of the dock watched as Paguseus flew further and further away into the sky.

“See you around, Marshal.” He said before leaving.

The Archivist who stood next to StoneColt walked to Twilight.

"Are you ready, Princess?" The Archivist asked.

Twilight turned smiling at both of them.

"Yes. Let's all go home." she replied.

The Archivist nodded her head to Twilight who stood up and soon walked away with by her side. Yet, the thought about the illusion Twilight was surrounded by continued to puzzle the Archivist. However, sensing happiness within Twilight’s smile, that illusion subsided. Later that day, a celebration was held in Canterlot Castle, honoring Twilight and her team of ponies for their bravery into stopping the Bronco-Titan. While being honored, Twilight stepped forward and whispered to the Princesses ear. Hearing her words, she smiled.

“In addition to honoring these brave ponies, I would like to ask not only in this throne room, but all of Equestria to pause for a moment of silence as we remember the fallen mare, Amethyst Crystal who gave her life by sacrificing herself to defeat the Bronco-Titan.” Princess Celestia announced.

The ponies throughout the castle, bowed their heads in respect. Twilight was proud at that moment as she thanked Amethyst in her mind. As ponies stomped on the floor, a massive party was set up in the courtyard, with music, balloons, and cake. Pinkie Pie could only hop around in happiness, singing and dancing. The evening hours soon approached, concluding the celebration only to continue with Pinkie Pie blasting throughout the castle. Twilight and her friends thought the never end and soon went along with it. Finally, ending at midnight, ponies returned to their homes to live on with their normal lives. On the way to her Castle, Twilight carried the sleeping Spike on her back to her room. Laying Spike on his bed and covering him with blankets, she threw herself on her own bed happy that she was back home and Equestria was once again at peace. She gazed upon the sof her castle wondering if Amethyst survived since Paguseus mentioned the Element of Space teleports the user to a different location off planet. Surprisingly, Paguseus sensed how much it would be a danger to the young mare that he interchanged its location to a place where both can be at peace. Closing her eyes, she smiled sensing that Amethyst laid next to her unconscious father on a peaceful garden, located in the land of the Griffons. Twilight shed a tear of happiness that Amethyst survived and immediately fell to sleep peacefully. As Twilight slept, the Archivist stood nearby her balcony and flew down to her home. She too thought Amethyst was dead, but now that Twilight was able to sense her presence, the Archivist felt reborn with positivity. However, one thought continued to haunt her. What power does Twilight possess that no pony knows about? Is it good or evil? All she can do is wait and see.

Epilogue

As the night sky shined over the calm, blue sea of western Equestria, a darkness grew below its haunting depths. Far below its surface, whales sang to one another miles and miles apart, school of fish swam calmly in an orderly fashion. Yet, deeper and deeper, the temperature and light soon began to dim in the great abyss, having no a pint of light shining down. Through those depths, strange fish with lantern antenna’s blinked through the abyss, as a sense of direction, until one shined at an unusual scaly creature. Blinking and blinking quietly, with only a few bubbles, the creature moved only an inch, making the fish much more curious.

Closer and closer the fish blinked, observing the scaly creature, until it finally stopped blinking. Within a second, the creature roared out, echoing throughout the ocean, reaching to almost the surface of the water. Something far below the surface had awoken from a long sleep and now its vengeance will soon turn the tide…

Prologue

“Xenxus’ raid on Canterlot was perhaps one event that caught us severely off guard, however I believe this is only getting worse. Yet, thanks to the assistance of Master Timaeus, Xenxus defeat came without any more harm. Now sealed thinking it’s over, I have come to realize I had more questions than I do with answers. Something was seriously wrong. How he ended up deep within the abandoned Tower of Kronos, I have no idea. Most importantly, how in the name of the Queen did he escape Tartarus? Especially passed Cerberus?

For that matter, Xenxus, the “stupid” one of his brothers…well, technically not stupid because of how he is known for surprises; orchestrate a jailbreak. Unless…Khaoios predicted it and knew he was gonna be put in isolation…No, it can’t be…More questions, less answers. Something was terribly wrong. Worst case scenario, Xenxus wasn’t the only one that left Tartarus. His brother, Titannus, but he hasn’t been seen which I question, “is it a good thing or bad thing”...I don’t know. My concern is to find what happened and resolve this problem without ponies getting hurt. Only thing is…are we fully prepared…”