Note: The song Halloween by Aqua really got me going on this story, and I used it for inspiration at the beginning.
The Doctor was working in the console room while John slept. The TARDIS was passing calmly through the vortex, the ambient light from the ceiling flickering occasionally as electrical charges that built up in the vortex passed through the TARDIS.
While they had been in a market the Doctor had spotted a replacement dial for the manual flight stabilizer, one that was closer to that of the original TARDIS console than the large and obtrusive crank handle she had had to repair it with when the original broke. She had just finished installing it and stepped back to see how the console looked with the change. She crossed her arms and scrunched her nose as she observed it - it didn't look right. Rather than make the controls look better, it just looked weird now in the midst of all the other odd bits she had used to fix the controls over the years.
The Doctor sighed and resigned herself to switching the components back, when all of a sudden the phone started to ring. She jumped, the TARDIS otherwise completely silent. She stared at the phone that sat on the other side of the console in shock. She thought back to the London Blitz and the gas mask child, which was the last (and only other) time the phone had rung. It ddring'ed again, and she tried not to think as she walked around to the other side of the console and picked up the phone gingerly, holding it up to her ear. She didn't say anything or make a sound, waiting for something to happen on the other end.
She was hoping that maybe she had imagined it, that maybe she needed another sleep cycle, when a grainy voice carried out of the speaker and into her ear.
"Remember me?" It sounded like a male voice, the Doctor didn't recognize it - and she had a very good memory.
"Sorry, you have the wrong number," she said.
"No I don't, Doctor," the voice said.
She paused in surprise before replying. "Alright, let's try this again. Hello, and who are you?"
"I'll tell you what I am, if you like." The Doctor stayed silent, waiting. "I'm coming to get you." The Doctor couldn't help but let out a huff of indignation. "You're in your TARDIS, aren't you?" it asked. She stayed silent, and then the mono-dimensional control handle sparked to her left. She turned her head to focus on it, and saw some of the controls start to turn and move on their own. Her eyes widened, and she opened her mouth to say something - she wasn't sure what - when the voice beat her to it. "Do you have one of your little pets with you?"
"JOHN!" the Doctor yelled, moving the phone away from her ear and covering the mouthpiece against her leg. When there was no answer in a couple of seconds she called her name again, slightly louder. "JOHN!" she could hear the panic in her voice the second time.
"What is it?" she heard John's voice over the double thump of her heartbeats. It was faint, being from another room, but it appeared that the TARDIS had moved his door closer to the console room so that he would hear her.
"YOU NEED TO GET OUT HERE NOW," she said, gripping the phone tighter in her hand, still pushing it against her leg.
"Alright, just give me a-"
"RIGHT NOW JOHN," she said, trying to make her seriousness clear in her voice.
A moment later a disgruntled John staggered out of the hallway that led to the rest of the TARDIS, looking very much like a colt in the way his limbs flailed about as he regained his balance. His flopped flat on one side, and he was dressed only in his goofy bow tie covered pyjama pants. His eyes met hers across the console room.
She raised the phone back to her ear, and she saw his eyebrows furrow when he realized that she was using the phone. "What do you want?"
"Always so concerned about your little pets," the voice said with a deep chuckle. "But neither of you can run from this."
The Doctor watched as the controls continued to move on their own, trying to analyze what they were trying to accomplish. "I'll ask you one more time: what. Do. You. Want?"
All of a sudden the console caught fire in front of her, and she jumped back away from the flames, the phone's cable extending to compensate. Sparks began to come out of some areas of the wall. She tried to pinpoint what wiring would be behind each spark, but the voice on the phone distracted her. "I want you to die." She heard a click as the voice hung up. A few moments later the cable melted and fell down to her side. She lowered the phone away from her head.
"Doctor?" John said from behind her. She turned her head to look at him. "What's going on?"
She looked down at the phone in her hand before dropping it on the floor, taking a step back from the console as the flames intensified. She squared her shoulders and looked up at him. "I don't know," she said, looking over her shoulder at the flaming console as her mind ran through all the possibilities she could think of. "Someone's controlling the TARDIS, somehow," she said. "But that's impossible. No, it's not. Time Lords - call them back - not this much control," she said, turning her head away from the flames that were slowly wicking away at what she had worked so hard to fix, her mind continuing to race.
"Doctor?"
"I'm thinking John, give me a minute," she said as she brushed her hair away from her face and ran her fingers through it.
"The hallway's moving."
"What are you talking about, it can't-" she started to say, but when she looked up at the back wall of the TARDIS she saw that John was right: the hallway was moving. Or rather, the wall was moving around the door frame, the circles moving from left to right as if the door wasn't there at all, causing it to look like it was the hallway moving. The Doctor turned in a circle, taking in every aspect of the room as she did so. Three-eighths of the way through her turn, she came to a startling conclusion, but she completed the turn to make sure.
The console room was shrinking.