Rainbow found the complex. She watched the activities going on from her bird's-eye view in the clouds. Guards were stationed on the roof and on the ground to protect the complex from intruders.
Fluttershy must be inside. Rainbow looked around the complex for a way in. There were air ducts on the roof... but snipers had been placed up there. That way was out of the question.
Could she fight her way in? She considered it then quickly brushed that thought away. She wouldn't make it far; there were too many guards. Whatever was going on here, they didn't want anyone to know.
"One step at a time," Rainbow told herself. She needed to get over the fence that surrounded the complex. It would be easy to just fly in, but flying around was an easy way to get spotted. She would have to stay grounded to get in... or not. Rainbow noticed a tree limb hanging over the top of the fence, with no guards around it. She quickly flew down from her clouds and into the tree. She inched her way through the leaves and branches to the one limb she needed, climbed it to the edge, and dropped down to the complex. Then, she quickly ran to and hugged a nearby wall for cover, using extreme caution. Stealth was never her strong suit, but she had no choice.
She noticed a door to her left and reached a hoof out to its knob. However, before she could touch it, it began to move on its own. Rainbow hid behind the opening door and watched as a guard walked out. He didn't notice the rainbow pegasus right behind him and continued to walk towards the fence. Rainbow stopped the door before it closed completely and rushed inside. She was in.
The door led her to a long, office-like hallway. She walked down the hall and ended up in an office area. Cubicles were everywhere; some empty, some not. Luckily for Rainbow, the humans at the desks were too caught up in their work to notice her. She looked around the office, and noticed two hallways leading out of the room not counting the one she came from. She slowly crept around the cubicles and entered one of the halls.
She slowly walked down the hall, watching and listening for anyone. Signs were hanging beside each door in the hall, but the language on them was indecipherable to her. She kept walking until she got to the final door at the end of the hall. She tried to open it but it wouldn't budge. There was a card reader beside the door. The light on the card reader was red, and she figured that meant it was locked.
Rainbow knew that she would have to get a keycard. She walked back down the hall when she heard talking in another room. Rainbow would have normally looked for a hiding spot, but this was different. She understood this language. She reached up a hoof and turned the knob. Finding that it was unlocked, she slowly and silently opened the door. Inside, a man in a red beret was looking out a window and talking on a radio.
"The final stage is about to begin," the man said into the radio. Rainbow looked around the office and saw a knife on the man's desk. She slowly approached the knife. "Our enemies won't see this coming. It's too perfect," he said to the radio. Rainbow picked up the knife. "We'll speak again soon," he finished, and clicked a button on the radio. He sat down in his chair, still unaware of Rainbow. She positioned the knife in her right hoof then struck.
Rainbow placed her left hoof over the man's mouth and the knife by his throat. The man panicked a little at first but after feeling the blade at his throat he calmed down.
"I'm going to let you speak, but no screaming. Got it?" Rainbow said in a harsh tone. The man nodded. Rainbow lowered her left hoof and the man let out a deep breath.
"Who are you?" he asked, but after seeing the hoof holding the knife, altered his question. "What are you?" Rainbow ignored the questions.
"The room at the end of the hall. You're going to help me get in there," Rainbow ordered. The man couldn't get over the horror of his current situation and just nodded. He slowly reached into the front pocket of his uniform and produced a keycard. It was black and white with black numbers printed in the white section. "Thank you," Rainbow said. She took the card with her left hoof and slowly put the knife away. The once the knife was out of sight the man let out a sigh. Rainbow quickly moved the knife back to his throat.
"If you EVER tell your friends I was here... I'll kill you," Rainbow growled. The man nodded nervously. Rainbow set the knife back on the desk and ran out of the office. She ran back to the keycard door and used the card. The light turned green and a lock from inside the door was released. She opened the door and found a staircase, which led down to a dark area. But somehow, she knew that this was the right way. She considered going back for the knife... but she knew she couldn't use it. She could never bring herself to kill somepony... or human, in this case. Even if she could, where would she carry it?
She descended the stairs to find a small room with a concrete floor and walls. There was a couch and some chairs here, along with a door to her right. But those things didn't concern her. Right in front of her was an elevator. She walked inside and looked at her floor options, but they were all in that strange language that was on the signs. So, she clicked the button closest to the bottom, hoping it would take her to the lowest floor. Rainbow recalled that in some spy books she had read, there was always some sort of top secret item on the bottom floor of the enemy's complex. Perhaps that was what Fluttershy's human friend was after, and maybe that was where Fluttershy herself was at. Rainbow braced herself for whatever was on the other side of those doors, but before they opened, the elevator stopped.
"I can't be all the way down yet!" Rainbow said out loud. And she was right... someone else had stopped the elevator.