Twilight's study room was a complete mess, but that was of no concern to her. Why take the time to tidy up when history-changing scientific breakthroughs were about to occur? In light of that, details such as appearance or even basic hygiene seem irrelevant; Twilight hadn't even showered or brushed her teeth for two days. Instead, she had gotten straight to work after waking up earlier the next morning. Her disheveled mane warranted no thought while papers filled with hastily scrawled notes surrounded her. Some were on the floor, on her desk, and even on the ceiling thanks to anti-gravity spells. Twilight's recently discovered but as-of-yet “officially” unnamed spell was active upon the room, coating it with glowing colors—predominantly purple.
Twilight groaned as she scanned the papers levitating in front of her. She had hit a roadblock of sorts, and wasn't sure how to proceed.
Spike chose that moment to walk in carrying a plateful of pancakes. "I thought you might like to eat breakfast in here," he said as he held out the plate. "I made them just the way you like them."
Twilight didn't even turn around. Instead she kept her attention devoted to her science. Idly, she stroked the wall to her left with magic, leaving behind a luminescent purple stain. She studied it for a moment, frowned, and turned back to her notes.
"Twilight, I brought you pancakes," Spike said, his voice louder than before.
Twilight picked up a blank sheet of paper with her mouth and began to gently drag it along the wall she had touched with magic.
Spike rolled his eyes. It seemed only the most desperate of measures would get Twilight's attention now. But before Spike could act, Twilight suddenly noticed him.
“Spi—oh, there you are, I was just about to call for you. Could you do me a favor and make me emotional?”
Spike blinked twice. "What?"
"I'm trying to figure out why the magical bi-planar luminescent particles have different colors," Twilight said. "You would think that my magic would be pink since that's the color my horn emits, but instead I always get purple. I'm trying to see if there is a correlation between emotion and color."
"So you want me to do something that will get a strong reaction from you?" Spike asked incredulously.
"More or less. Either positive or negative, I've yet to try either one."
"Well, I did just make you a batch of your favorite pancakes." Spike held up the plate again. "You want some?"
"Oh, thank you Spike!" Twilight said gratefully. "I would very much like—"
Spike spat green fire at the pancakes, instantly reducing them to ash.
Twilight's grateful expression melted. "Oh."
"You gonna do your thing or what?" Spike prompted.
Glumly, Twilight turned her attention to the wall and touched it with magic; an identical purple blotch painted the spot.
"Aw, nothing," she said with a sigh. "And I didn't even my get my pancakes."
"Oh, uh, I can make more," Spike said quickly. "Sorry about that."
“No, it’s fine, I asked for it. Tell you what, how about you make some more and I'll come downstairs to join you,” Twilight suggested. “I should probably take a break from this anyway.”
"Deal." Spike turned and exited the room.
Twilight took a few minutes to stack up her notes and then made her way downstairs to the kitchen. A fresh batch of pancakes was already on the table, still steaming hot; Spike stood at the counter, flipping more pancakes with practiced dexterity.
Twilight levitated up a book and began reading as she ate. Just before she could consume the last bite, there was a knock on the front door.
"Kind of early for a library visit, isn't it?" Spike raised an eyebrow.
Twilight stiffened as she remembered she still hadn't showered or brushed her teeth. "Could you get that, Spike? I'm not quite ready for visitors yet." She dashed up the stairs while Spike went to answer the door. After freshening up in record time, Twilight came back down to discover a clearly distraught yellow pegasus eating pancakes. Instantly, she felt bad for keeping one of her best friends waiting.
"What's the matter, Fluttershy?" Twilight asked with concern.
"Oh, Twilight, it's the most awful thing." Fluttershy sniffed. "Some of the animals have been driven out of the forest. Their homes have been destroyed."
"Destroyed? By what?"
Fluttershy shook her head. "I don't know. I didn't dare go into the woods myself. I was hoping you could come with me and help."
"Of course I will," Twilight promised. "We'll go right now."
"I'll clean up breakfast and open the library," Spike offered.
"Thanks, Spike. Hopefully, we'll have this fixed before too long," Twilight said. "After you, Fluttershy."
Fluttershy sniffled again. “Thank you, Twilight.”
As they traveled towards the outside edge of Ponyville, Twilight tried to imagine what could have destroyed the animal's habitats. It couldn't have been a forest fire, or someone would have seen smoke. A rampant monster from the Everfree forest was a possibility, or even some naive campers. If it was the latter, Twilight had in mind to give them a good scolding. If the former, she was willing to let Fluttershy take the reins; Fluttershy had always had a way with animals, monsters included.
When the two mares reached the woods, they began traveling inward between the trees. Minutes passed by as Fluttershy led, following some sort of path Twilight couldn't detect.
“Here we are, Twilight. Look at all those poor trees.”
Twilight gasped. It was a large rectangular area absent of trees. Much to her fascination, long wooden beams stretched across the area overhead, with the tree canopy sitting on top of them. Twilight deduced that from above, the clearing was undetectable without sacrificing space below the canopy. There were more wooden beams all over the place, shaping the outlines of a construction in progress. Nearby, larges piles of dirt sat by giant holes in the ground inside the structure. Twilight also spotted tools such as saws and shovels, safely tied to some of the upright beams by chains and padlocks.
"What is this place?" Fluttershy wondered.
"A construction zone," Twilight answered. "One that someone went through great lengths to hide from the rest of the world. It's so deep into the woods, no one might ever have found it if it weren't for your animal friends."
"Does that mean somepony is building something here illegally?" Fluttershy asked.
Twilight shrugged as she started to walk forward to get a better look. "Could be."
Twilight came to an abrupt stop as she recalled what had happened the last time she recklessly entered a crime scene. It had only been because of Big Macintosh that she had narrowly avoided an ambush. For all she knew, criminals could be hiding in the holes.
Twilight lifted up a nearby rock with magic and hurled it into one of the holes in the ground. No reaction. A little more confident, Twilight approached the framework and and glanced around.
"Fluttershy, how old do you think this thing is?"
"Well, um, it can't be too old." Fluttershy flew up to better inspect the framework. "The wood looks freshly cut, and there's piles of wood dust on the ground that hasn't been washed away by rain yet. And those tree tops on the, um, top are still green. Cut off from the rest of the trees like that, they won't stay that way."
"Maybe the tree tops are fake?" Twilight suggested.
"The leaves look real, and it still has its bark," Fluttershy replied. "I've never seen anyone do this to trees."
"Well, we can either wait for someone to come back, or we can trace them with my, um… shoot, that still needs a name… We can trace with them with my magical bi-planar luminescent particle finder spell."
"That's a very good name," Fluttershy said a little too quickly.
Twilight closed her eyes while she mentally prepared the spell. Once her thoughts were gathered, her horn glowed to life. The white sphere exploded outward until about half of the clearing was in its radius. She scowled slightly; she had been hoping for something bigger.
Regardless, Twilight began to study her surroundings. The first thing she noticed was that Fluttershy's wings were glowing light blue.
"Oh, that's interesting. Your wings are magical," Twilight said.
"That's... great I guess?" Fluttershy said hesitantly as she glanced her own wings. "They'll turn back to normal soon, right?"
"They will. Even sooner if you step outside of the spell's range," Twilight said. "Could you do me a favor and fly around? I want to see if I can track your progress through the air."
Fluttershy did so, and Twilight was pleased to see specks of blue light trailing behind the pegasus. Not only that, but the underside of Fluttershy's hooves also glowed light blue. Twilight smirked as she realized the irony. Originally she had thought her spell would only be useful for unicorns. Now, it seemed, it actually worked better for tracking pegasi and earth ponies. To the best of Twilight's knowledge, unicorns were untraceable unless they used magic. Of course, assuming it worked on earth ponies was based off the examples of Big Macintosh and the criminal they had caught together. Twilight hoped they were the norm, not the exception.
"Well? Does it work?" Fluttershy asked as she gently landed in front of Twilight.
"Lift up your hoof real quick," Twilight requested.
Fluttershy did so, revealing a faint blue smudge of light underneath.
"It works, even better than I expected." Twilight turned her attention back to the crime scene.
Five different colors were present, which presumably meant five different ponies had been there. There were spots all over the ground, on the tools, and on the beams. Twilight also noticed that some of the spots on the ground were smaller than others, basically specks like Fluttershy's wings had given off. The five different colors were too abundant for Twilight to guess their routes on the scene, but she spotted what appeared to be a trail of glowing green blots leading away from it.
"There. Right there," Twilight said as she pointed a hoof at the trail. "If we follow that, we should find one of the construction workers for this place. When we find him, we'll have answers."
“I hope we don't interrupt him doing anything important.”
Twilight smiled to herself. Only Fluttershy could be concerned about someone who had destroyed animal's habitats for a secret building project. Twilight took the lead, using her spell like a flashlight to follow the suspect. Twilight and Fluttershy conversed as they went, but the longer they traveled the more weary Twilight felt as she strived to maintain the spell. Unlike last time, the suspect was evidently not located nearby.
Just moments before Twilight wanted to call for a break, she and Fluttershy at last came upon a log cabin from behind. The two mares circled around to the front and approached the front door. Twilight exchanged a glance with Fluttershy, took a deep breath, and knocked.