PART ONE
MAGIC
1
Twilight Sparkle smiled as she glanced around the room. Almost a full house. Definitely a good sign that, even on a day of celebration like today, most of her students attended anyway. Showed just how good a professor she was.
“Welcome, everyone,” she spoke into the magical receiver, hearing her own voice broadcast across the large lecture hall.
She had almost said everypony there. Force of habit from when Canterlot wasn’t as culturally diverse. Now, as opposed to a class of mostly unicorn ponies, she had pegasi, earth ponies and unicorns, along with zebras, gryphons, minotaurs, diamond dogs, merponies (using talismans to gain the ability to walk on land, of course), thestrals (“batpony” was considered a derogatory term in this day and age), and even the odd changeling, their colourful chitin shining in the light.
Taking a breath, she prepared to begin her lecture.
The door burst open.
Expecting a late student, she turned to glare at the entrance. What she saw surprised her.
Shining Armor, in full Royal Guard regalia, galloping in, a desperate look in his eyes.
“Twilight!”
Giving a sheepish smile at her students, she spoke a quick, “Be right back,” then calmly walked over to her brother.
“Shining, what is going on?” she asked, a frown on her muzzle. “You know I’m teaching very important things now.”
“Twilight, I’m so sorry about this,” Shining apologized, his horn glowing pink as he carried the folder beside him. “Celestia insisted on calling for you.”
Twilight was happy with her life as a professor of Advanced Magic at Canterlot School for Gifted Unicorns. She was comfortable with it. And now, here was her brother, and by proxy, Celestia herself, demanding that she return to her old life of adventure.
“No, Shiny,” she said, determined to not let this intrusion stop her lesson. “Whatever she needs, she can get anywhere else.”
The stallion sighed. Speaking in hushed tones, he explained the situation.
“A threat has been made against Canterlot. Luna’s been kidnapped, and six explosives have been placed around the city. They’re gonna tear it from the mountainside.”
Twilight opened her mouth to protest with the little-known fact that magical explosions have an upper limit to the damage they can cause.
“And before you say anything,” Shining interrupted her, “we’re not talking magic. This is… this is science.”
She balked at her brother’s words. “B-but… but science of that kind doesn’t exist! Everypony knows that! You can’t spontaneously turn matter into energy without magic!”
“Twilight, you have to understand. We don’t take any threat of this nature lightly.”
“But why me?” she asked.
Shining sighed once again. “I can’t tell you. I’m sorry.”
But he knew why Celestia had demanded Twilight herself.
She thinks you’re behind it.
Twilight glanced around the lecture hall, at all the faces staring back at her, some worried what the interruption was, some more angry that she wasn’t getting on with it.
“Twilight, please.”
Saying nothing, she nodded, and began to walk back to her podium.
“Class dismissed.”
2
Watching as the students left the room — in a neat, single-file line — Twilight Sparkle stood beside her brother, assessing the letter and images that had been given to Celestia just ten minutes prior.
“This could easily be faked with simple magic,” she reasoned. “There’s no need to take this seriously.
“Twilight, this is a terrorist threat. We must take it seriously,” Shining spoke firmly. “If we don’t, all of Equestria could be in danger without us doing anything about it.”
“Okay, okay, I get it. You can’t dismiss this. But… but why me…” she repeated.
Shining held his tongue at that, not wanting to reveal Celestia’s true motivation behind asking for her own former student.
“I don’t know, Twilight.”
Her ears perked up, and she turned to face her brother with a slight glare. “Just a moment ago you said you couldn’t tell me. Now you say you don’t know at all?”
Shining outwardly rolled his eyes despite the minor panic inside his mind, and began to trot out of the classroom. “Never mind that, Twily. Just follow me.”
Twilight frowned, but obeyed him, walking along behind her brother.
Trotting down the hallways of the sprawling building that was Canterlot School for Gifted Unicorns, the two ponies analysed the images and note before them as they walked.
Shining looked at his sister curiously. “What’s on your mind?” he asked, then instantly grimaced at the look the mare shot at him.
“You know perfectly well what’s on my mind,” she answered, pointing a forehoof at the picture floating in front of her. “This can’t be true. Why would anypony do anything like this?”
“Well, as you can see,” the Captain of the Guard pointed out, “he has certain… demands.”
Twilight read over the note a second time, frowning even more so than before.
“But all books in the Canterlot Library are freely available,” she reasoned. “Celestia believes in freedom of information, even when it’s something as dangerous as… as science. All you have to do is request them, and the librarians will determine whether your reason for needing them is good enough.”
“Not exactly ‘freely available’, then. Maybe whoever is threatening us had already sent in a request and got denied.”
“Then his reasons for needing them weren’t good enough,” Twilight said firmly.
“Besides,” Shining spoke, ignoring his sister’s tone, “not every book is available to the public, even through a request system. Some of them are so restricted, even the highest-ranking professors can’t read them.”
That stopped her in her tracks.
“You mean… there are books that even I can’t access?” she asked, to which her brother simply gave a nod. “That’s… that’s ridiculous! How could anything be that restricted?”
“Those books contain information on some very dangerous things,” Shining explained. “Things like how to create explosives powerful enough to wipe entire kingdoms off the map.”
Understanding, Twilight nodded, though her expression didn’t lighten up. “Okay. Fine. Some books are super dangerous. But…” She sighed, and shook her head, beginning her steady trot once again. “Never mind. Let’s just do what Celestia tasked us with.”
“Us? Sorry, Twilight, but this is too dangerous a mission to risk the Captain of the Royal Guard on,” Shining said solemnly.
Her eyes went wide. “You mean I’m going at this alone?”
“Not quite alone…” he says with a smirk as the pair breached the main entrance of CSGU.
“Twilight!” came a familiar voice, one she hadn’t heard in years, as a mint-green unicorn mare galloped over to her, wearing a black suit. Behind her, calmly walking, a cream-coloured mare in a similar outfit, her two-tone mane neatly styled and her eyes hidden behind sunglasses.
“Lyra!” Twilight said with a bright grin, wrapping a foreleg around her withers in a hug. “I haven’t seen you in so long! How’ve things been?”
“No time for that,” the other mare spoke as she caught up to them. “We are on an important mission here, Lyra.”
The minty mare rolled her eyes as she pulled back from the hug. “Come on, not even for catching up with an old friend?”
Twilight smiled as she regarded the other pony. “Lyra, who is this?”
“Oh!” Lyra perked up, turning to face her old classmate. “Twilight, this is Bon Bon, my wife,” she explained.
“We’re with SMILE,” Bon Bon interrupted before any further conversation could happen. “We’re here to help you on this mission. And, sorry for my partner’s excitability,” she apologised, lifting her glasses to glare over at her spouse. “She’s new to this.”
3
Twilight stared at the cream-coloured mare, unable to believe what she was hearing. SMILE? Unlike most civilians, she was familiar with the organisation: A group so secretive that only the highest-ranking of them even knew what the acronym stood for.
SMILE itself is helping me?
Clearly, this was a very dangerous mission, if Celestia had sent two Mares In Black — as SMILE officers were commonly known. Then again, she thought, Bon Bon did say that Lyra was new to this. Maybe that meant they weren’t taking this all that seriously.
Or maybe…
The other possibility hit Twilight like a magical bolt to the chest.
Maybe they deemed her disposable…
Trotting down the streets of Canterlot, flanked by the two mares from SMILE, with her brother bringing up the rear, Twilight made her way along the Royal Mile, as the main street leading to Canterlot Castle was known.
Soon enough, they arrived at the massive gates to the castle, two guards assessing them. One nod from Shining, though, and they were immediately let inside, no questions asked.
“Thank you, sirs,” Twilight said out of habit, walking through the gate. Considering her status as a Princess of Equestria, she likely would have been let in quickly enough anyway, even without assistance from her brother. She wasn’t sure about the other two mares, though. Even with their uniforms, they might have been held for a while — impersonating an officer of SMILE was easy enough, though the repercussions were disastrous. And a while was something they certainly didn’t have, judging by Bon Bon’s eagerness to get going.
Wandering through the halls of the castle, Twilight got her first good look around the majestic building in years. She hadn’t visited her old mentor since she’d received her job as a professor at the — now privately-owned — School for Gifted Unicorns. Her heart ached with nostalgia.
Soon, the four ponies arrived in the throne room where Celestia was due to greet them. Her eyes widened as she admired the imposing stained glass windows, depicting Equestrian history. She particularly focused on the one representing her own ascension. It seemed so long ago now…
“Welcome, Twilight,” a gentle voice spoke, breaking her stupor. Celestia herself stood before them, smiling down at her former pupil. Twilight smiled back.
“Celestia…” she said with a curtsy, “it’s an honour to stand before you once again.”
The Princess laughed, lifting Twilight’s head back up with a forehoof. “No need for that, Twilight. We’re friends, remember?” Her tone and expression soon darkened, though. “Besides, there’s no time for pleasantries,” she said firmly. “Equestria is under attack.”
Twilight nodded.
“Shining has briefed you on the situation,” she said, then turned to Shining, “haven’t you?”
“Of course, my Princess.”
“Good.” Celestia gave a brief smile, which quickly disappeared. “Now, Twilight. Do you understand the importance of this mission?”
“Yes, Princess.”
“You understand that, if you fail in your mission, Canterlot will be destroyed and Equestria will be without a capital to defend itself from?”
“Yes, Princess.”
“And you understand that time is of the essence if we are to stop these explosives and save my sister?”
“Yes, Princess.”
“Then go.”
With a nod, Twilight turned to walk away. Then, pausing, she turned back to her old mentor. “Go where?” she asked sheepishly.
Celestia smiled. “Your old room. It’s been put back just the way you had it.”
Twilight’s eyes widened. “My old place atop the Ivory Tower?”
The Princess nodded.
With a grin, Twilight began her trot through the castle grounds, heading for her old home, followed closely by her partners. Shining Armor, though, walked back to the Royal Guard headquarters.
Galloping along behind her, Lyra held out the pictures and note in her magical grip, hovering just in front of Twilight. Analysing them as she ran, Twilight racked her mind for where the explosives could be hidden. Those photos could be taken anywhere. They don’t even show any landmarks! Either this pony is a fake, or smart about not letting us find any of these.
Then, she stopped in her tracks. Looking over the pictures again, her eyes went wide. The countdowns…
The lowest one was approximately three hours. Factoring in time of delivery, that meant…
She didn’t get to finish her thought before an explosion directly in front of her rocked the mountainside city of Canterlot. Twilight gaped at the result.
The impressive height of the Ivory Tower no longer existed on the skyline.
Her old home was gone.
The threat was real.
4
Galloping to the site of the explosion, dodging and weaving through the castle’s crowds, Twilight and her company soon arrived at the Ivory Tower. What they saw was devastating.
The tower was gone, having collapsed under its own weight soon after the bomb’s structural damage. Debris lay everywhere, white stone scattered about the place, the orb at the peak of the tower having crashed down and shattered into hundreds of thousands of pieces.
Twilight stood there, muzzle hanging open in shock. Her old home… the one she had lived in for years before she had moved to Ponyville… gone.
“Right,” said Bon Bon, after a good minute of silence from her temporary leader. “Let’s, uh. Analyse the site. See what we can find out.”
Taking a few seconds to register what she had said, Twilight nodded, taking a few shaky steps closer to the site.
“Twilight?” her old friend Lyra asked, concerned. “You can sit this one out, if it’s too much.”
“No, no, I’m… I’m fine.” She gave a shaky smile. “Besides, Celestia assigned me to this,” she said with determination, walking up to the center of the explosion.
Bon Bon was busy searching the site for the device used, using her earth pony strength to move the stones, soon finding the spent casing of the explosive among the rubble. “Lyra, can you bag this for me?” she called out, and her wife was immediately by her side, pulling out a plastic specimen bag to contain the evidence.
“What are we bagging this for?” she asked. “It’s dead.”
“Yes, but there might still be some of the explosive left inside it,” Bon Bon explained, “and we can analyse that to find out exactly what we’re dealing with.”
Lyra nodded in understanding, holding the bag in her magic.
Meanwhile, Twilight Sparkle searched the rubble, finding book after ruined book that brought back memories — there were some that she had been unable to transfer over to the Golden Oaks library when she had moved to Ponyville. The callous destruction of such precious material brought a tear to her eye. Never mind the property damage, she thought. Buildings can be rebuilt. Some of these books have been out of print for centuries!
Sighing, she trotted back to her partners in crime-solving. “Find anything?”
“We found the device,” Bon Bon confirmed with a nod. “We’ll take it back to the lab to have it analysed.” She began to walk away, her spouse in tow.
Twilight just stood there, unsure what to do. Are they just… going to let me into SMILE HQ? After a few moments of Bon Bon staring at her from a few steps away, waiting for her to follow, she figured out that, yes. They were just going to let her in.
5
“As you can see,” the stallion presenting the analysis data said, pointing a forehoof at a large screen, “this substance is a mix of various powders, including sulphur and charcoal. Most of it, though, we can’t recognise.” He nodded at the unicorn casting the screen spell, who switched to a pie chart, showing how almost 80% was some unrecognisable material. “It appears whoever is responsible has synthesised a new, highly volatile compound using some advanced form of alchemy.”
Twilight knew what that meant. “Not alchemy,” she explained. “Chemistry. Turning something into something else with no magical assistance.”
“But that’s impossible!” the stallion exclaimed.
“Not impossible, just highly forbidden. Not even I can access books about it.”
Bon Bon spoke up, having walked into the room just moments prior. “You can now,” she said, slipping a lanyard around Twilight’s neck, an ID card clipped onto it. “Welcome to SMILE, Princess Twilight.”
Twilight stared at her, shocked. “What?”
“I said, welcome to SMILE.” Bon Bon smiled. “You’re an honorary member. You can access any documents you wish, even ones restricted to the public, for as long as this investigation lasts.”
Twilight’s expression soon turned to a big grin. This was huge. She could read anything! Everything! All the books ever published were hers to read!
Lyra laughed as she walked in behind her wife. “Don’t get too excited now, Twilight,” she teased. Seeing Bon Bon’s serious expression, though, she soon dropped the light tone. “Remember, we have an important mission.”
Twilight nodded.
“Right, where to first?” she asked, which was met with a blank look from Lyra and Bon Bon. “What?”
“Twilight, you’re the one in charge of this operation,” Lyra explained.
“Oh.” She paused, thinking. Her old library was ruined, though that wouldn’t have been much help anyway, considering the books she needed to research were highly restricted. Then she remembered where she was.
“To the SMILE Archives!”
6
The SMILE Archives were huge. Easily a few hundred acres in size, the Archives held almost everything in Equestrian possession. Treasures from faraway lands, magical weapons, and, most important to Twilight, hundreds upon thousands of books. Including, in a restricted section, all of the most forbidden tomes and scrolls.
Standing in this restricted section, Twilight, Lyra, and Bon Bon searched the shelves for anything that might help them.
Twilight groaned at the mess the shelves were in. No kind of order at all. Not by subject matter, not by title, not by author. Come on, she thought. How hard could it be to sort all this? The Starswirl System isn’t that complicated!
Half an hour had passed by the time she found the section she was looking for. “Alright, here it is. Chemistry,” she said to her partners, who soon stood by her side. Scanning the shelves, pulling out book after book, she flicked through each in a matter of seconds, using magic to store the information in her mind.
Halfway through the fifth book, she abruptly stopped.
A neatly-written note sat inside, tucked in to the spine. She recognised the writing as being the criminal’s.
Hello, Princess,
I see you’ve figured out how I was able to achieve such massive damage. Chemistry, of course, is one of the highly forbidden Sciences, and the one capable of causing the most physical damage.
Since you’ve come this far, I think I’m going to let you in on the rules of my little game.
1. You have one hour between each explosion.
2. I will leave hints spread around Canterlot, pointing to the next device.
And, the most important rule,
3. Have fun.
Yours,
Master Mind
15-5-1-20-15-8-8-14-25-20-13-1-23-15-15-1-20-8-21-13-14-20-1-4-5
Twilight’s eyes went wide as she saw the final line. “He’s leaving clues for us! He’s giving us a chance to find the bombs before they go off!”
Bon Bon raised an eyebrow. “Why?”
“He’s calling it a game,” Lyra reasoned, reading off the note. “He’s toying with us.”
Pointing a forehoof at the string of numbers, Twilight smiled. “There’s our hint to where the next bomb is!”
“Coordinates?” Bon Bon asked.
“No, Bon Bon, it can’t be that easy.”
Twilight read over the line of digits over and over again. Then, the pieces fell into place.
“Look,” she said, pointing to one of the numbers. “The largest number is 25. That means it could be a letters-to-numbers cipher!”
Her horn lit up brightly as she cast an air-writing spell, tracing the shapes of letters with her hoof as she unraveled the code.
OEATOHHNYTMAWOOATHUMNTADE
The three mares stared at the resulting word.
“Well,” the cream-coloured pony spoke after a good few moments. “That makes no sense.”
“But… but I was so sure that…”
“It must just be a set of coordinates, then,” Lyra said, reading over the note once more.
“But the highest number is 25…”
25… 25…?
Her mouth fell open.
“25! There are only 25 letters!”
“So?” Bon Bon asked.
“It’s a square number!” Twilight exclaimed, sitting on her haunches and using her forehooves to rearrange the letters into a five-by-five grid.
O E A T O
H H N Y T
M A W O O
A T H U M
N T A D E
Lyra and Bon Bon tilted their heads in confusion.
“It’s a cipher invented by an emperor of the ancient Roaman Empire,” Twilight explained. “You write the code in a square grid, from top to bottom, then rewrite it from left to right!”
Rearranging the letters once again resulted in a familiar phrase.
“I don’t get it,” said Bon Bon.
But Twilight understood. Whoever was behind this knew far more about her and her friends than she had thought. She read over the phrase once again.
OH MANEHATTAN WHAT YOU DO TO ME
PART TWO
GENEROSITY
7
Reading the message over and over, Twilight stood stunned.
OH MANEHATTAN WHAT YOU DO TO ME
She recognised it, of course, as the first line of the song Rarity had sung once she arrived in Manehattan, on the day she had received her Key to the Chest of Harmony. This pony must know me and my friends well, thought Twilight. Probably someone close to me…
She closed her eyes and thought about who might have motivation to destroy Canterlot. Taking a few minutes to go through the list of everyone she knew, she came up blank. No one she knew would want to do anything like this…
A voice snapped her out of her meditation. “Twilight?”
“Wha, huh, yes?”
Lyra giggled. Bon Bon did not. Instead, she looked very worried.
“It’s been almost an hour since the explosion. Have you figured out where the next bomb is?”
Twilight froze. An hour already?! “W-well, uhm,” she stammered. “Not… really…?” she offered with a sheepish grin. The Mare in Black was not amused. Sighing, she thought over what to say. After a good few moments, she spoke. “Something to do with Rarity.”
The two mares stared at her blankly, expecting her to continue.
Silence.
“…go on, Twilight.”
“That’s all I have!” she said desperately, starting to panic, pacing circles around the place.
“Well, we’ll need to narrow it down somehow.” Lyra watched her trot around. “Does Rarity own an apartment in Canterlot?”
A spark shone in Twilight’s eyes. That’s it!
“No!” she said confidently.
Confused at the disparity between her tone and her words, Lyra and Bon Bon waited for an explanation. It soon came.
“But she does own a clothes store! In the Shopping District! Canterlot Boutique!”
Eager to get going, Twilight started to trot off, with her friends in tow. Then, reality sank in for the three fillies.
The Shopping District was half an hour away.
8
They weren’t even close when they heard another explosion in the distance, smoke and fire billowing up from the far away Shopping District. It took twenty minutes to reach the site where Canterlot Boutique once stood, and a further five to weave their way through the crowd that had gathered.
Another scene of destruction lay before them.
The shop and those surrounding it were a smoking wreck, shards of glass from the windows scattered around, having injured a few citizens as they flew away from the blast. Thankfully, no one was seriously harmed — the shards had somehow avoided the critical points, as if by magic.
Twilight and her friends stood before the site of the bombing, eyeing the damage. All of Rarity’s hard work and dedication up in smoke… She knew there was no time to mourn, though — almost half of the deadline for the next bomb had already passed. They had to act fast.
Scanning the area, they found something graffitied onto the side of the building.
Twilight analysed it intently. Could this be the next clue?
“What are you looking at?” asked Lyra. “It’s just some incomprehensible graffiti. By somepony called...” She stepped closer to the apparent signature. “#X?”
“That doesn’t make any sense,” Bon Bon reasoned. “Vandalists don’t tend to sign their work.”
But there it was, a signature, right at the lower right of the piece.
“It hasn’t faded or bled into the stonework,” Twilight observed. “That means, whatever this graffiti is, it can’t be more than a few hours old.”
“Okay, so we find some kind of weird graffiti at the crime scene that was painted just a few hours ago,” Bon Bon said, standing by her side. “That doesn’t necessarily mean the two crimes are connected.”
But Twilight wasn’t listening. She could swear she’d seen something like this before. And that signature… what could it mean? Casting her air-writing spell once again, she began to think.
“It could be simple code-writing,” she stated, drawing out the code in the air in front of her using her forehooves. “One symbol per letter. But figuring it out with such a small code would be complicated…”
“What?” Lyra perked up an eyebrow. “Wouldn’t it being longer mean it would be more complicated?”
“Well,” Twilight began to explain, “with a longer code, you can analyse it for patterns, like common symbols which could represent common letters. Whereas with something short, it’s much harder to find patterns.”
Lyra nodded in understanding. “So how do we figure out what it says?”
“Well, last time, Master Mind gave us just enough information to solve the puzzle,” Twilight said, thinking back to the note in the book. “A simple letters-to-numbers cipher is much easier to break than a substitution cipher — code-writing — though.”
“So, then, there must be something we’re not seeing here,” Bon Bon continued, understanding the path her leader was following.
No one said anything for a few moments, deep in thought.
“Bon Bon,” Twilight spoke after a short while. “What was that you said earlier?”
“About?” the cream-coloured mare tilted her head questioningly.
“The signature.”
“That it doesn’t make any sense,” she repeated. “Why would somepony sign their crime?”
Thinking over it, Twilight realised something. “There’s nothing that shows that it’s a signature. It could be part of the clue!”
As she wrote the signature in the air beside the code, something clicked. She realised where she recognised the code from. It was such a simple code, one she had played around with when she was a filly.
“A pigpen cipher!”
“A what?” Lyra asked.
“It’s a modified version of the pigpen cipher,” Twilight explained. With a wave of her hooves, the air before her was blank once more. She began by writing the criss-cross symbol twice in a row, then the diagonal cross twice below it. Then, she filled in each square with a letter.
“Every letter is enclosed like this, and you write the symbol corresponding to the enclosure the letter you’re encoding is in,” she described. “But it looks here,” she pointed to the very top corner, following the swooping line as it flowed down the side, “like the artist decided to combine elements of another cipher as well. I can’t remember the name of this one, but it’s just as simple. You extend one of the lines if you’re referring to the dotted variants, instead of adding a dot.”
“Then why is there a dot there?” Lyra pointed out the dot above one of the V-looking symbols.
“Probably because the artist couldn’t fit an extended line in, so they instead added a dot. Combining two different ciphers like this is sloppy, but at least it’s consistently so,” Twilight said with a little chuckle.
“So what does it say?” Bon Bon asked.
“That’s what I’m figuring out right now,” Twilight answered.
Writing in the air, she started to decode the cipher. R-A-I-N…
“Rain?” Lyra read. Twilight shushed her as she wrote out the rest of the code.
R-A-I-N B-O-W-D A-S-H
Twilight stared at it.
“Okay, so we found one of Rainbow Dash’s fans’ vandalism.” Bon Bon watched her leader as she stood stupefied by the writing in the air. “What’s it got to do with the investigation?”
But Twilight wasn’t listening. She understood what the criminal was doing now. The bomb at her home, the one at Canterlot Boutique, and now this…
He’s going after me and my friends!