The Princess, and the Lord of Time.

by Thunder Quill

Rating: teen
Tags: Dark, Alternate Universe, Romance, Original Character, Adventure, Twilight Sparkle, Anthro, My Little Pony: Friendship is Magic
Length: 4729

Twilight Sparkle is The newest Princess of Equestria, when she was young her best friend was a Unicorn named Thunder Quill. They were inseparable, but when he had to move away, she swore off friends forever. Now he's back, but he holds a secret.

Twilight Sparkle is the newest princess of equestria, but when she was younger she had a best friend who she was inseparable from. When he had to move away though, she swore friends off forever until she met the others in Ponyville, but she never forgot Thunder. Now he is back with a secret, one that could change everything.

Amazing Editing Job Done By Pen Brush, a great author, and an even greater friend, please, check out her works.

Published 2014-04-29 13:40:01 UTC
Last updated 2014-04-29 13:40:01 UTC

Chapter 1

Celestia’s beautiful shining sun rose over the tops of the trees in Ponyville as it made its way across the morning sky. The light that shone through the Golden Oaks library reaching a certain lavender princesses resting place, awakening her from a well earned sleep. Twilight sat up on her bed and stretched out her body, hearing a few tiny cracks as she unfurled her wings. She looked out the window near her bed, wondering what exactly the day would have in store for her, and she smiled.

She climbed out of bed and quickly tidied up her bed, before she walked into her bathroom. She looked around, the marble tiles on the floor cold under her hooves. There was a walk in shower with a see through door, with a pristine toilet opposite it, the sink beside it with a small mahogany cabinet above it. Twilight slowly took off her nightgown and set it down on the sink as she pulled open the shower door. She twisted the shower handle and watched the water cascade down, waiting for it to heat up as it splashed onto the floor of the shower and went down the drain.

Once the water was hot enough, she walked in and closed the door. As the water flowed down her body, she let her mind wander. She mostly thought about what was inside the box that the Tree of Harmony had created and how, if somepony were to attack, she would protect Equestria with her friends. All of these things came to mind, but another thought was there along with it, of one of her friends that she had lost so suddenly before she had even met her Ponyville friends. She hadn't even gotten to say goodbye to Thunder Quill.

Twilight knew he wasn't dead, but he was forced to move away from Canterlot quickly and with no warning. She felt like she had been abandoned by the one who got her so interested in learning to begin with, being so young, and yet knowing so much. She had sworn off friendship with anyone after that, save for her big brother.

Her thoughts were abruptly shattered when the doorbell rang throughout the library. She sighed, it was probably Rainbow looking to get the next Daring Doo book this early in the morning. She turned off the water and grabbed a towel to dry herself off as she walked back to her room. Once she had thoroughly dried herself completely, she went into her dresser and grabbed a black T-shirt and stretchy pants that matched. She wasn't sure why, but she had been wearing a lot of black clothes recently.

Twilight quickly walked down the steps back to the main room of the library and opened the front door, “May I help you?” she asked, looking at who it was who had interrupted her shower.

A tall, well built white unicorn stallion looked back at her and smirked, “Hi Twilight. Still sleeping till noon?” he asked, in a rather familiar, if somewhat deeper, voice. He had a spiky black mane that framed his black eyes, and he was also wearing dark clothing

Twilight looked at the unicorn, a little confused, “I’m sorry, but who are you?” she asked uncertainly.

The stallion frowned, sadness and pain deep in his eyes, “Never mind, it was a mistake to come here, you don't remember me. Sorry for wasting your time.” he said as he stepped down from the doorstep.

Something in Twilight’s mind clicked into place and she gasped. She grabbed ahold of the stallion’s arm with enough strength for

him to wince, and pulled him back, “Thunder?” she whispered wonderingly.

The stallion smiled, “One and only.” he whispered back.

Twilight stared at him, before she threw her arms around him suddenly and hugged him tightly. Thunder was a bit surprised, but he just smiled wider and hugged her right back for a few minutes in each others brace, enjoying the happy reunion.

Twilight broke the hug and looked up into his eyes, “What are you doing here, what happened to you?” she asked

Thunder sighed, “It doesn't matter what happened. I decided I wanted to live here, and I heard from some ponies in town that Princess Twilight lived here in the library, so I decided why not visit an old friend?” he said.

Twilight looked disappointed with Thunder not explaining his disappearance, but the rest of his answer made her excited, “You're moving here? That’s great, that means we can catch up after so long! What are you doing today?” she asked.

Thunder shrugged, “I got nothing I really need to do, so nothing.” he said.

Twilight smiled, “I can show you around town and you can meet all of my friends then!” she exclaimed, grabbing ahold of his arm and pulling him out the door.

Thunder started losing the feeling in his arm as she pulled him, and pain, “Ow, ow, ow, Twilight let go!” he pleaded.

Twilight stopped and let go of Thunders arm sheepishly, “Sorry.” she said, a slight blush in her cheeks.

Thunder rolled his arm in its socket to get the feeling back, “Its alright, but that ascension must have increased your strength a lot!”

Twilight giggled, “Yeah, maybe.” she said.

“So where do you want to go first? I was going to go to get something to eat before I knew you were here, so I’m famished.” Thunder said, his stomach growling an affirmative.

Twilight hummed thoughtfully, “I know where we can go.” she said, taking Thunder’s hand. They walked down the street in silence, as Twilight brought Thunder over to a multi colored building that looked a little bit like a gingerbread house.

Thunder stared at it for a second then read the sign next to the building, “Sugarcube Corner?” he asked.

Twilight nodded, “One of my friends works here, her name’s Pinkie Pie, I’m guessing you know who she is.” she said, leading him into the bakery.

Twilight waved at the five other mares, all being different colors and race. One was a white unicorn who looked to be a noble, two of them were earth ponies, one all pink and bubbly and the other being orange with a bit of a southern look, and the last two were pegasi, one a cyan color with a rainbow mane, and the other a bright yellow with a pink mane that covered one of her eyes.

“I would like you to meet an old friend of mine, this is Thunder, Thunder, they are Pinkie Pie, Fluttershy, Rainbow Dash, Applejack, and Rarity, some really close friends I made since coming to ponyville and becoming the Elements of Harmony.” Twilight said, introducing them all.

Thunder looked at them all with a bit of puzzlement, before he smiled at the welcoming looks they gave him.

Applejack walked over to Thunder and put out her hand, which Thunder took as she shook it in greeting, “Welcome ta Ponyville pardner.” she said.

Thunder nodded, “Nice meeting you, I've heard a lot about the Elements of Harmony.” he said, before he noticed something odd, “Interesting, you're all wearing black as well.” He said thoughtfully, looking at the identical clothes each wore.

Twilight frowned, “Odd, how did we not notice that?” she wondered, sitting down in a vacant seat as Thunder pulls up one beside her. She looked over at Thunder as he sat down and saw he was staring off into space, “Are you alright?” she asked, putting a hand on his shoulder.

Thunder blinked and turned to face her, “Yeah...I’m fine, just thinking. I guess you want to know more about me and where I was after so long Twilight?” he asked, leaning back in his chair.

Rarity frowned, “Do you not wish to know about us Darling?” she asked.

Thunder smirked, “Oh everypony knows about the elements of harmony and their stories, but they do not know anything about what they had said during that time. You, Rarity Augustine Belle, in a bout of frustration at finding a rock to be your apparent destiny after being dragged for days by your horn, yelled ‘A ROCK?! That’s my destiny?! What is your problem horn? I followed you all the way out here for a ROCK?! UHG!!! Dumb rock!’ before a rainbow explosion shook the earth, broke your rock, and tied all six of you to each other as friends, and only got your mark after your talent show, the same explosion doing the same for the rest of you, with the marks that you clearly have today. Am I correct?” he asked, smiling at Rarities look of disbelief.

Rarity nodded slowly, “How did you know that?” she asked amazed.

Thunder smirked, “Lucky guess.” he said cheekily, “Now, what do you want to know about me?” he asked.

“How did you an Twilight meet exactly?” Applejack asked.

A shadow passed over Thunders face as Twilight looked down at her hands, “It wasn't the best circumstances, I will admit...” Twilight sighed.

Twilight closed her eyes, and a five year old Twilight was lying on the ground in front of her, reading one of her many favourite books, ‘Daring Do and the Gryphon’s Goblet.’

Twilight read quietly on a hill, the sun warming her back as she lied away from anypony else. As she read, three shadows appeared above her, obscuring the sun above her. Twilight froze in her reading, they were back again.

Twilight looked up, “Well looky here, if it’s not our good, magicless, friend Twilight Sparkle.” the ring leader of the three, a thirteen year old large gray earth pony , who had a jagged scar over one of his eyes, said.

Twilight scrambled up to her feet quickly, holding the book tightly to her chest, “Wh-what do you want?” she asked, trying to be braver than she felt.

The earth pony pouted, “Oh, why so rude? Give me that stupid book, you need to be taught a lesson on how to treat ponies.” he said, taking the book out of her hands. He looked at the cover and smirked, “Enjoy Daring Do? Not anymore.” he ripped the book into four pieces with his strength.

Twilight had tears in her eyes as she watched the destruction of her book, and in the next second she screamed when she was in the air for a second before she was pushed and fell down the hill. When she stopped at the base of the hill, bruised and battered, the bullies ran down towards her, laughing.

Twilight started crawling away from them, but was stopped as the earth pony caught up to her and slammed his food into her side with all his strength, the sound of a few ribs breaking making her scream. The earth ponies goons, a unicorn and a pegasus, dragged her roughly back to her feet, and held her arms behind her.

The earth pony smiled, “Trying to run away now? You really need this lesson taught.” he said, punching her in the side, again and again as she screamed. When he paused to look over his handiwork, Twilight had a black eye, a broken bloody nose, multiple broken ribs, and more bruises than he could count. He smiled as he brought his fist back for a final blow as Twilight struggled to stay conscious.

“Hey.” a new, very calm voice that the earth pony could hear rage behind, said.

He turned around to face the voice, and saw five year old Thunder. Thunder looked at the earth pony calmly, but his eyes were glowing bright like an angry fire, “What do you want shorty?” he mocked.

Thunder stared him in the eye, “For you to leave the poor filly alone.” he said.

The earth pony laughed, “Oh really? Who will stop us if we don't?” he asked.

“If you won't stop on your own, I’ll stop you.” Thunder replied, still in the same calm tone as before.

The earth pony snarled and turned to his goons, “Get him boys, show him nopony messes with us, especially not a shrimp like him.” he instructed. The unicorn and pegasus let go of Twilight, who was in no position to run, and charged at Thunder. The pegasus reached him first, and starting throwing a flurry of punches at Thunder. He landed a few, three to his head and one to his stomach, but to his surprise, Thunder managed to evade the rest of his advances, before he leaped backwards away from him in the air.

Thunder landed and wasted no time running towards the pegasus, pulling back his fist to punch him in the face, which he barely managed to block with an arm. he grabbed his arm and bend it behind his back, making him scream as it broke. Thunder leg go of his useless arm and hit the pegasus in the head with an elbow, knocking him out.

The unicorn, seeing this, hesitated in his advance and looked back at the earth pony, “GET HIM YOU IDIOT!” he screamed. The unicorn turned back and his horn glowed, bringing his hands up in front of him, sending a gout of flame at Thunder. Thunder kneeled down and his own horn glowed as the flames washed over him.

The unicorn stopped his attack, looking to be victorious, until the flames subsided and Thunder was safe behind a slightly weak shield forcefield, his mane slightly burnt and windswept.

Thunder put his hands down, canceling the spell as he stood up. He raised an eyebrow, “Battle of spells then? Alright.” he closed his eyes as he concentrated, his hands glowing as he builds up the spell. His eyes shot open as his hands glowed a blinding white and brought them up, a beam of light shooting out, hitting the unicorn in the head. The spell sent the unicorn flying backwards past the earth pony into a tree. The glow of Thunder’s hands died down until they were back to normal, the magic fading, taking away some of his energy as well.

The earth pony stood where he was, shocked, before he shook his head and frowned. He grabbed ahold of Twilight by her neck and held a knife against her skin, “Back off, or she gets it!” he yelled. Thunder stepped forward, before he stopped and gazed at Twilight, nodding slightly. His hands glowed as leaves blew past him and he disappeared

The earth pony laughed, “I guess your ‘hero’ despite taking out my possy, was nothing more than a coward!” he threw Twilight to the ground and leaned over her. She was so badly beaten and bloody from his previous attack that all she could do was lay there and whimper as he smirked, “Time to die!” he exclaimed sadistically.

A cough from behind the earth pony caused him to freeze, before he frowned and whipped around to face who it was, jumping up. Thunder looked back at him, his eyes blazed with fire.

The earth pony took a step back, before he regained his composure and smirked, he wasn't going to let a five year old get in his way, “You really can't take a hint can you?!” he yelled, running at him and slashing at Thunder with the knife. Thunder moved, but not before it cut him in the cheek, blood flowing out of the small cut. The earth pony kept swinging at him, nicking him once or twice on the nose, but not enough to gain a lead, “BUCKING STAY STILL SO I CAN KILL YOU!” he screamed, thrusting the knife at Thunders chest.

Thunder moved faster than he thought he could and got behind the earth pony, kicking him square in the back. He fell to the ground in a heap and groaned as Thunder turned him around so he was lying on his back and kneeled down,, throwing the knife away from his hand “Do you have anything to say to this filly?” He asked, indicating Twilight. The earth pony only glared at him and didn't respond. Thunder shrugged, “Alright then, times up.” he said, punching him square in the face, sending the older colt into unconsciousness.

Thunder stood up, holding his cheek as he bled, his hands burning from holding back the fire earlier and sniffed, blood dripping down his nose. He looked over at Twilight and rushed over to her, noticing that she was struggling to stay awake , concern clearly etched in his eyes as she fell unconscious. He stayed beside her as sirens went off in the distance and yelling came from the top of the hill as ponies ran down to them.

When Twilight woke up, she was greeted by a soft beeping beside her. Slowly her eyes opened and they immediately focused on the worried faces of her family standing over her in a hospital room.

Relief flooded their faces when they saw she was awake, “Twilly! Thank Celestia you're Ok!” her big brother, Shining Armour exclaimed, giving her a hug.

Twilight smiled as she hugged him back "H-hey." she croaked., her throat dry. She let go and lied back down in the bed, looking around for who was missing, “Where is he?” she asked worriedly.

Her father, Nightlight looked at her, a bit confused, “Who, that unicorn colt that was brought here with you? When the doctors had taken care of his cuts and burns, he wouldn't leave your side the entire time . He blamed himself for you getting hurt for some reason, kept saying something about being there sooner. He didn't eat or sleep the entire time, despite the doctors telling him he needed rest and we finally were able to convince the kid to get some food.” he said, smirking slightly .

As her father finished, the door opened and everypony in the room turned to look at Thunder as he entered. he looked around the room, awkwardly as everyone stared, a big bandage on his cheek, gauze around his hands, head and a bandage on his nose where he had been cut twice. He was holding a tray of food in his hands, despite them being wrapped in gauze.

When he noticed that Twilight was awake, he smiled and walked over to her, placing the food tray on the table beside her. “How

are you feeling? Better?” he asked quietly.

Twilight nodded, “A little bit. You saved me, thank you.” she said.

Thunders cheeks glowed red, “No problem.” he said, looking down.

Twilight smiled, “I don't think we have properly introduced ourselves with what had happened, I’m Twilight Sparkle.” she said.

Thunder lifted his head and looked into her eyes, “I’m Thunder, My name is Thunder. its nice to meet you” he said, smiling back.

Twilight looked around the table at her friends as she finished the story, a sad smile on her face, “We became best friends after that, and he would visit me in the hospital until I got better just so I would have somepony to talk to when my family couldn’t visit.

He amazed me with all the knowledge he knew.” she finished.

“What horrid brutes those colts were!” Rarity exclaimed, as Rainbow rolled her eyes, muttering under her breath how she could have taken them.

Thunder nodded, “They were, and they never bothered Twilight again after that, the judge made sure of it.” he growled.

Twilight looked over at him, “After I was able to leave the hospital, we did everything together, and he taught me some self defense that he had done just in case I needed it again.” she said.

Rainbow Dash folded her arms, “So thats why you were so awesome at fighting the changelings off during the wedding invasion?” she asked.

Twilight nodded, “Yes, I guess you could say that’s why.” She said.

Thunder’s face darkened for a second as he glared at the table, before his stomach reminded him of why they were at the bakery to begin with as it growled loudly, he looked up and chuckled, “Enough about the past, how about we get something to eat?” he suggested.

Pinkie jumped out of her seat and bounced in place, “Ill get us some!” she exclaimed, running into the kitchen, Thunder watching her go.

When he turned back, Rainbow was right in front of his face, “So what you been doing since you left Twilight?” she asked.

Thunder frowned and looked down, “Traveling all over Equestria and feven outside of it” he said, gently pushing her away.

“Who did ya go round with?” Applejack asked.

Thunder’s face hardened, “My dad.” he said through gritted teeth.

Rarity tilted her head, “Is something the matter darling? Are you having problems with your father?” she asked.

Thunder shook his head, “No, I left him by himself awhile ago and haven't talked to him since then.” he said.

“W-what happened, I-if you don't mind me asking...” Fluttershy whispered quietly, hiding behind her mane.

Thunder sighed, “We disagreed about everything. We couldn't compromise on anything.” he said.

Applejack leaned against the table, “Have ya ever thunk ah mendin fences with im?” she asked.

“A few times, but he wouldn't accept it, maybe someday though.” he said, shrugging.

Applejack was about to say something again when Pinkie Pie ran back out of the kitchen with plates full of cookies and muffins,

“Eat your growl away!” she exclaimed, putting the plates down in front of everypony.

Thunder smiled, letting his mood evaporate into the air, “These look delicious Pinkie, thank you.” he said, picking up a chocolate muffin and biting into it, extra vigor in his personality.

Rainbow leaned against a wall as she bit into a cookie, “So what exactly are ya doin here in Ponyville anyway besides visiting Twi?” she asked, staring at him.

He looked up at her as he swallowed a piece of his muffin, the sweet chocolaty taste going down his tongue as he smiled, “I actually decided to move here, been traveling all over for so long, I decided it would be better to settle down, where better then a small town full of nice ponies?” he asked.

“Do ya got any place ta stay sugarcube?” Applejack asked.

Thunder shook his head, “I have enough bits to buy a house around here, but will need a job afterwards to keep it.” he said.

“Did you by chance bring furniture along with you to make the house a bit less empty?” Rarity asked.

He shook his head again, “No, I didn't bring anything but enough bits for a house, I was planning to get furniture as we go along.” he said, biting into his muffin again before he froze, realizing what he had just said.

Twilight tilted her head, “Who is we? You said you were alone.” she said.

Thunder sighed, “Remember when we were kids and I told you I was an only child?” he asked. Twilight nodded so he continued, “Well, it turns out I actually do have a sister, she is younger then me and we ended up meeting while I was traveling around, I don't know how I didn't meet her when I was with my dad. She is kind of rude, cynical and doesn't care for other ponies that much, but when she needs to, but she has a heart of gold when she wants to.” he said, smiling.

Twilight frowned, “Where is she? She wasn't with you when you came to the library, did you leave her alone?” she asked.

Thunder frowned, “No, she went to town hall to buy the house for me, I told her to come to the bakery once she was done.” he said.

"Why would you tell her to meet us here?" Twilight asked him.

Thunder shrugged, “I was hungry, and she took the bits before I could suggest we go eat first, so I told her to meet me here.” he said.

Applejack frowned, squinting at him, but before she could say anything, the front door opened and the bell above it rang. A purple unicorn with deep green eyes and a light blue mane stood in the doorway, glaring at the bell as she unzipped her burnt black leather jacket.

Thunder turned and smiled at her, “Girls, I would like you to meet my sister, Quill.” he said.

Quill looked away from the bell and walked over to the table, “Proclaim it to the world why don't you...” she muttered, looking at the ponies at the table.

Thunder rubbed his eyes, “Pull up a seat and sit down. Did you get a house?” he asked.

Quill looked around and her hands glowed a bright purple, encasing a nearby chair and bringing it over, before she set it down next to Thunder and sat down, “The mayor is incompetent, but I managed to have her sell me an available house thats near the library.

No furniture like I wanted, but its suitable I guess if you like that sort of thing.” she said, leaning back and putting her hooves on the table.

“We will figure the furniture thing out later, don't worry.” Thunder said, handing her a muffin.

“Your near the library? That means you're close to me.” she said smiling, extending a hand to Quill, who stared at it, “Its nice to meet you Quill, I’m Twilight Sparkle.”

Quill took her feet off the table and leaned forward in her chair, biting into her muffin, “Sure, nice. So your Twilight? Did my brother tell you about the time-”

Thunder cut her off, “Can I talk to you for a second in private Quill?” he asked quickly.

Quill glared at him, annoyed he had cut in to her conversation, “Why?” she asked.

Thunder stood up, “Just come on.” he said.

Quill rolled her eyes and dropped the muffin onto the table, before she stood up and followed him outside.

Quill slammed the door shut and turned to Thunder as he leaned against the building, “What?” she asked.

Thunder sighed and looked her in the eye, “Why would you say that?!” he exclaimed.

Quill sighed, “Say what? What did I do to-” she stopped as her eyes lit up with realization and she smirked, “You haven't told them yet, have you?” she said, chuckling.

Thunder sighed, hitting his head against the wall, "Yeah, I haven't said anything, sue me."

Quill rolled her eyes, “You're hopeless, you know that? A hopeless stupid romantic who can't even talk to a mare.” she said.

Thunder sighed, exasperated, “Shut up, I'll tell her, I will, but until then, don't tell any of them anything.” he said, looking Quill in the eyes.

Quill folded her arms and glared at him, “Hmmm, alright, Ill give you a week, starting now, and if you don't tell her, I will. “ she said threateningly.

Thunder put a hand to his head, “Seriously, a week? Come on, give me some more time for Celestia’s sake!” he exclaimed.

Quill shook her head, “A week, not a day more, not a day less. At exactly this time a week from now, if you haven't said anything, I will.” she said.

Thunder put his head in his hands and shook himself, putting his hands down, “Alright, fine, lets just go back in. Thy are probably wondering what we are doing.” he huffed, walking past Quill back into Sugarcube Corner.

Twilight looked up as Thunder and Quill walked back in, Thunder glaring at his sister, “Are you ok?” she asked.

Thunder nodded and took his seat next to Twilight, “Right as rain.” he said, shooting glances at Quill beside him.

Applejack looked between the siblings, “So, yer lookin fer ah job?” she asked. Thunder nodded and prompted her to continue, “Ah could always use some more help on tha farm, if ya want, what do ya say?” she asked.

Thunder thought about that, before he turned to Quill, “It sounds good, what do you think?” he asked.

Quill sighed as she studied her muffin, “Farms, how fun...yeah, it sounds fine, it beats whatever we were doing before.” she replied.

Applejack smiled, “Tha’s great, ya can start tomorrow, does tha sound aright ta ya?” she asked.

Thunder nodded, "Yeah."

Twilight smiled, "Great, now that everything has been fixed for you, lets eat." she said, biting into her muffin, as everypony else ate as well, unaware of what was going to happen.