OK, pointless legal bumf time; If I didn't create it, I don't own it. Simple as.
On a more specific level, Doctor Who is the property of BBC Worldwide. Puella Magi Madoka Magica is the property of studio SHAFT and Aniplex.
Next, content warning. Like all my previous work, this fic contains definite Self-Insertion/Sue and probable Canon Defilement. If any of this offends you, stop reading NOW. Although why are you reading fan-fiction if you get offended by Canon Defilement?
Finally, a note on chronology, and how this fits into canon; for the sake of argument it takes place between Planet of the Dead and The Waters of Mars, and between timelines four and five.
Puella Magi Madoka Magica/Doctor Who: Red Eyes and Blue Boxes.
Chapter One
UNIT-SEA Headquarters, Kyoto, Japan.
March 14th, 2015
The corporal read the file that had landed on his desk several weeks ago.
"Strange disappearances; unexplained suicides. Since when was it in our remit to cover these?" Despite being in Japan, he spoke English with a hint of a British accent; The South East Asian contingent of UNIT was one of the few to be truly multinational, rather than just having a few international personnel on secondment, although that was the case for him and a few others from nations beyond the Pacific rim. There was a sense of lacking sleep behind his pale brown eyes; he'd been pulling overtime trying to finish up the paperwork from the last big incident.
"The local police gave up trying to explain it, and there are rumours of supernatural circumstances going around." The Private he was discussing the matter with was Australian, with dark red hair and blue-brown eyes. "And there's more. Every single one of the victims had a mark etched into their skin on the side of their neck."
"A tattoo?"
"Nope. This mark went all the way down and was even burned into the bone."
"So, what're you thinking? Aliens?"
"Possibly. That's what it usually turns out to be, at least when it's not a cult."
The corporal sighed and picked up the phone.
"You know the CO's never going to agree to something like this."
Mitakihara, Japan.
March 20th, 2015
"I still can't believe the CO agreed to this." The corporal drew the Type-73 jeep up to the blockade, away from where the investigation team had started work. He killed the engine, opened the door, and stepped out, pulling his scarlet beret out from under the epaulette on his right shoulder, the SIG-Sauer P226 holstered on his right thigh clicking slightly as he did so. It was a chilly night, with the first few spots of rain starting to fall. The investigation team were examining what appeared to be a pair of suicide-jumpers laying sprawled on the ground.
"OK, what've we got?" The corporal asked one of the soldiers already on perimeter duty.
"Two victims, both apparently jumped. No one's been sent into the building yet in case whatever it was that made them do it's still inside." The soldier took a quick note of the ID cards attached to their tactical vests; Corporal Rose and Private Conway.
"They got a mark?"
"Yup. Right side of the neck, same as all the others."
"OK. We got a scientist on the ground yet?"
However, before he could get an answer, an explosion ripped through one of the upper floors, sending a cascade of debris raining down into the street.
Corporal Rose grabbed his sidearm from its holster, along with a flashlight from his belt as he ran towards the building. There wasn't time to retrieve their rifles from the back of the jeep.
"All points, hold position. Greyhound two-six and three-four moving in." He broadcast over the radio in the left shoulder pocket of his vest.
The third floor was quiet, and almost completely undamaged beyond fairly normal dilapidation considering the building was abandoned; there was nothing to suggest that a bomb had gone off. However, one room was different. Within that room, the walls were scorched, with several blown right out, one of which revealed the scene outside. Inside, the two soldiers found a single girl facing the hole. She was wearing a strange white, grey and black dress, with long black hair reaching down to her thighs. There was some sort of buckler attached to her left arm, and a softly glowing purple gem on her left wrist, which stretched over the back of her hand. Corporal Rose brought his pistol up, the flashlight in his left hand underneath it.
"Freeze!"
On hearing this command, the girl turned around and took one step back away from them, towards the opening. Her purple eyes seemed to be both piercing and determined, yet there was no light in them; it was almost like they were staring down a walking corpse.
"Under the authority of the Unified Intelligence Task force, I'm ordering you to halt!" He shouted.
"No, you aren't." She replied, and with a click, she vanished.
Conway holstered his own pistol.
"Who was she, and where did she go?"
"I don't know, Private. You tell me." Jon clicked his radio. "Greyhound Two-Six to Greyhound Three-Nine; Did anyone just pass you at the perimeter?"
"Negative."
"Looks like we have a problem then."
Suddenly a noise began to spread through the area, a noise which sounded like someone running a door key down a piano string, and a noise that was accompanied by the wind picking up around one specific spot.
"Make that two problems."
The blue box finished materialising outside the barricade, and a few seconds later a man with messy dark brown hair stuck his head out, to be greeted by five UNIT soldiers. One of them reached up and activated his radio.
"Greyhound control; Greyhound Two-Six. Get Colonel Carter on the horn; We've got a blue-box situation."
The man looked round.
"I don't suppose any of you would mind telling me where I am? Or when, for that matter?"
The lead soldier sighed.
"You're in Mitakihara, Japan. It's March the twentieth, 2015." He raised his right arm and checked his watch. "Just after quarter-past eleven in the evening."
"Right-o. So what's UNIT doing out here?"
"I could ask you the same question. We're investigating possible mind-control induced suicides. You?"
"Chasing a temporal blip. Something around here fudged around with time for an instant. Anyway, who are you?"
The soldier snapped a salute.
"Corporal Jon Rose, sir."
"I don't know how many times I have to tell you people this, Corporal, but I don't like being saluted. And besides, you don't need to call be sir."
The Doctor passed the Sonic Screwdriver over one of the walls in the room where the girl had vanished.
"Hmm... Traces of nitrocellulose, potassium chloride, graphite and ammonium nitrate."
"Smokeless gunpowder and agricultural fertilizer. Probably whatever was in the bomb that went off in here." Jon passed his flashlight over the scorch patterns on the wall.
"Very good, Corporal. But that doesn't explain why I picked up a temporal blip out here now, does it?"
"No, but the fact that someone vanished into thin air more-or-less where you're standing right now might."
The Doctor scanned the floor.
"You're right. High concentrations of chroniton particles over here."
"Enough to explain what was screwing with time?"
"Possibly." The Doctor slid the screwdriver back into his jacket. "Question is, what has the ability to do something like this. Anyway..." His voice perked back up again. "You mentioned something about mind control? Haven't seen a good bit of mind control in ages!"
Jon lead the Doctor out to a mobile autopsy lab set up in a tent. Inside, both victims were laid out, and the pathologist was stood to one side. Having examined both of them, the Doctor straightened up.
"So, what do you think?"
"Well..." The Doctor started, cocking his head to one side, "...You were right. They certainly jumped, and there's traces of some pretty bizarre energy in the nervous system."
"But you said you couldn't mind-control a person to commit suicide; the human survival instinct's just too strong."
"How'd you know about that?"
"Case files from the Sycorax incident nine years ago. It's in the statement the PM's aide gave after the fact."
"Very good, you've done your homework. It's not strictly true though. It is true that you can't order a person to kill themselves with mind control like the Sycorax did. But you can make a pretty strong suggestion and let nature take its course."
"So what about the mark?" Jon tilted the head of one of the victims, exposing the marking on her neck.
"Never seen anything like that before. Whatever it is, the energy seems to be concentrated around it."
Jon sighed.
"So we've got an unknown entity that can make people commit suicide, and a strange girl who can screw with time running around. Why do I get the feeling these two things are connected?"