This story is based on a dream I had a couple of weeks ago wherein the Doctor ended up in cold storage in Torchwood (a la To The Last Man). Most of this story will be told through the Doctor's point of view.
Disclaimer: Doctor Who and Torchwood: Two things I do not and never will own. Go figure.
When UNIT had been assured that there was no remaining threat and had kindly escorted the Jones' back to the ground, Jack and the Doctor were left alone.
Jack was afraid to touch the Doctor, the disturb his grief--he had been clutching the Master to his chest for the past two hours, and aside from his sobbing slowing from loud and wet to dry and heaving, he was showing no improvement of psyche. And as much as it hurt to watch him mourn such an evil man, Jack knew the Doctor needed this. They had been friends once, after all, and the Master had spent the past year(that now only existed for a handful of people) stomping on the Doctor mentally, physically, and emotionally. So he sat back and let his old friend grieve.
After another hour, he slowly approached and then gently pried the Doctor away from the other Time Lord's body. The older man immediately latched on to Jack, no longer crying but still trembling alarmingly. Jack guided him towards the little maintenance closet where the TARDIS was hidden, allowing him to cling. Before they were far down the first corridor, though, they were intercepted by two men that Jack knew the look of all too well.
As the men drew within speaking distance, the one in the lead calmly drew a black wallet out and flashed its contents at Jack.
"Torchwood Two." he said solemnly, and Jack suddenly had a very bad feeling.
ONE YEAR LATER
The Doctor drifted slowly into a state of awareness. The first thing he noticed was that he was on Earth--he could feel the planet spinning, after all, and no planet had a velocity quite like good old green-and-blue.
The next thing he noticed was that he was cold. Then he tried to open his eyes and discovered that he was lying directly under a very bright light.
Approximately three minutes later, as the noise of people talking quietly began to seep into his brain, he put the pieces together, realized he was lying on an operation table, and promptly had a panic attack.
They had killed him on an operating table once, and it had hurt so badly that the only thing worse was Gallifrey burning--
"Doctor! Doctor! Somebody help me hold him--Doctor, calm down, it's me--"
It was Jack. Jack would help him. "They're going to cut me open!" he rasped frantically, and was rewarded with a lift into warm arms.
His frantic trembling calmed as Jack rocked him gently. "You're all right, no one's going to hurt you, you're fine." The Doctor could feel Jack's single heart beating as fast as his two.
"'S cold." he mumbled into Jack's chest. He was groggy and didn't know where he was, but Jack was there and that was relatively safe. He noticed that Jack's chest rumbled when he laughed, even when it was strained. "You'll warm up, I promise."
"Why'm I cold?"
That hand that had been resting on his back moved to the back of his neck and rubbed. The Doctor thought it felt nice and allowed it to distract him while another pair of hands dressed him in what felt like his favorite suit.
"Jack!" he whined impatiently as he was lifted again and his feet met the floor. He swayed for a moment, almost unable to support his own weight, but Jack caught him and supported him so that by the time they go to the spiraling staircase that led up from the examination room, he was steady on his feet. By the time Jack had led him to a modestly furnished office area, he was feeling very awake and eager to move around. He didn't protest when Jack sat down and pulled him into his lap and rubbed his back to sooth the trembling that came from manic energy, though, because Jack was still warm and he was still so very cold.
"This isn't the Valiant." he said curiously, resisting the urge to kick his legs against the chair.
"No. You're in Torchwood. My office, in fact." the Doctor felt Jack rumble in amusement as he took new interest in the small office, turning his head around to look and then squirming to get free of Jack's arms and explore.
Jack took him on a tour, showing him everything from the cells to the vaults to the insides of all the machines, and even let him touch some of them, and then Jack introduced him to his team and Martha was there, which was a delight in itself.
He asked Martha about her family, which made her start crying. Contrite, he took her hand and apologized for being insensitive, but that only made her cry harder and not even a joke about his current regeneration's rudeness seemed to calm her down.
Jack took her aside and they disappeared while a team member named Tosh showed him a computer program that she had written. It shouldn't have been seen on Earth for another hundred hears, but Tosh had written it herself without the aid of alien technology, so the Doctor was proud and he told her so. "Oh, you're absolutely brilliant. You're a star. I understand why Jack always bragged on you so much." And even though Jack had never specifically mentioned the members of his team during their time on the Valiant, the pleased flush on Tosh's face made the little white lie worth it. Usually they were.
It wasn't until Jack and Martha reappeared with pizza that he realized they had left the building.
They all sat at a big conference table--not just him and Jack and Martha, but also Tosh and another team member named Gwen and the man that Jack had been exchanging suggestive grins with all day who was wearing a black suit with a pink button-up underneath. His name was Ianto, and the Doctor thought he was really sort of adorable with Jack.
After dinner Martha got kind of sniffley again, and they made him lie back down on the operating table, which wasn't nearly as frightening with both Jack and Martha there. He felt like he was forgetting something, something important, but thinking was hard when Jack was massaging his scalp, even if it was just to distract him from Martha putting a needle in his arm.
"Doctor." Jack said gently.
"Doctor, I'm--we're--you're going to sleep for a while, okay? You remember this, don't you?"
"Sleep? Okay." he agreed contently. "A little nap. Nappity-nap-nap."
"That's not what I mean." Jack said helplessly. "Look--the reason you were cold--Doctor, I didn't have a choice..." Jack took a deep breath and tried to catch Martha's eye as she studiously concentrated on injecting various substances into the alien lying between them.
"You're going to sleep for a year, Doctor." Jack said finally.
The Doctor blinked up at Jack, who looked equal parts miserable and guilty. "Why am I here, Jack?"
Jack gave him a sad, brief smile. "We're protecting the universe from you."
He smiled back, feeling sort of sad himself. "Well, it's about time someone did."