Wow, this chapter refused to end. It just kept going. So sorry for the long update time! Arg...

Disclaimer: I don't own Doctor Who.

xxx

Rose and Martha stared down the way they'd just run as their minds raced.

"Oh my god they've got him," Rose said finally, "they've got the Doctor, we've got to go back!" she started to run back, but Martha grabbed her.

"No! We can't! They'll just get us too," Martha argued.

"Well what do we do then?!" Rose shouted angrily.

"We… oh I don't know! You're the one that works at Torchwood, you tell me!"

"I don't think I work there anymore…" Rose muttered. She pulled herself away from Martha and looked around nervously. "I don't even know what they'll do to him. The only aliens they've ever found have been dead, and they've always dissected them and done experiments and stuff."

"Well they're not going to do that to the Doctor, are they?" Martha said, "I mean, they wouldn't." Rose bit her lip apprehensively.

"I don't know," she said quietly. "I… I don't know." She put her hand over her mouth, but tried to act strong. "We've gotta save him," she said decidedly.

"Can't we just go into Torchwood and find him?" Martha suggested.

"They're after us, aren't they? If we go anywhere near there they'll get us." Martha nodded. The two women thought for a few moments, until Martha had another idea.

"What about Jack?" she asked, "he was in the TARDIS, and if they've taken it, shouldn't he now be in Torchwood?" Rose thought about this.

"You're right!" she said excitedly, "and they won't know to go after him, as long as they don't see him leave the TARDIS." She pulled her phone out of her pocket and hit the redial button. She held it to her ear and they waited as it rang. They waited for a few moments, until Rose pulled it away from her head and looked at it angrily. "Answer your bloody phone!" she shouted. Her hand dropped down to her side. She looked up at Martha. "Now what?"

xxx

Jack lay dismally on the floor groaning. He felt a throbbing pain rush through his head as his world spun. His hands reached up and grabbed his hair, as he curled slightly into a ball and waited until the throbbing pain died down to a dull ache. He could vaguely hear noises coming from somewhere in the distance, muffled by the sounds of the TARDIS. Well, at least that meant he was still in the TARDIS.

Reluctantly, he opened an eye and looked around. He then opened the other eye and pushed himself up. He sat on the floor, rubbing his head, trying to focus his eyes. As his mind seemed to start to work again he pushed himself to his feet, trying to ignore the sudden dizziness that was threatening to envelope him and went to the consol.

He waited for the TARDIS to tell him what had happened, watching the screen. An explanation flashed across it, confirming what he already suspected. The TARDIS had been transported via some sort of transmat, and judging by his splitting headache, it wasn't a very good one. He asked the TARDIS for their location, and found they were slap bang in the middle of Canary Warf, otherwise known as Torchwood.

His attention was pulled to the voices coming from outside. He turned the security camera on and watched on the screen as a group of scientists attempted to open the TARDIS doors using a number of different methods, ranging from using high-tech alien machines to trying to pry it open using a credit card. Jack smiled to himself. God bless the human race and their stupidity.

Suddenly he wondered if the TARDIS had been taken, had they taken the others too? He'd been unconscious from the transmat and he didn't know how long he'd been out. He pulled his phone out of his pocket and looked guiltily at the surprisingly high number of missed calls on it. He selected Rose's number from his contacts list and held his phone to his ear.

xxx

Martha and Rose looked around the area that the Doctor had been taken in. The guards had gone and there seemed to be no sign of them ever being there. Martha was walking around the space for any clues as to what to do, while Rose sat on a bench trying to ring Jack every minute or so.

"Any luck?" Martha asked.

"Nothing," Rose answered, looking at her phone with a mixture of anger, disappointment and slight confusion. Suddenly, the screen lit up as it started ringing. The two of them stared at it for a few moments, before Rose pressed a button and held it to her ear. "Jack!"

"Rose! Sorry, where are you?"

"Where are you? You were meant to protect the TARDIS!"

"Hey, wasn't my fault! One minute everything was fine, next thing I know I'm lying unconscious on the floor from a dodgy transmat. Are you all ok?" Rose paused for a moment before answering.

"They've got the Doctor," she said quietly, the emotion evident in her voice. Jack froze for a moment.

"How long ago was this?" he asked nervously.

"About twenty minutes," Rose answered. "We thought you might be able to save him, if you can get out the TARDIS without being noticed."

"Well I can't do that now, there's a bunch of guys trying to get in."

"They'll leave soon, once they realise they can't get in," Rose said, "they'll know they need the Doctor to get in. And knowing Torchwood they'll do anything to him until he agrees to let them in," she said nervously.

"And knowing the Doctor he won't ever let them in," Jack said, equally nervous. "Right, if I'm going to save him, you'll need to help. I'll put you on an earpiece and you guide me to where he's been taken. I'll leave just as soon as this lot do," Jack said decidedly. Rose agreed, and Jack sat on the chair, watching the security camera, waiting.

xxx

Not long later, Jack was wondering through Torchwood, following Rose's directions. He was wearing a white lab coat that Rose had said to wear, because apparently everyone in Torchwood wore white lab coats whether they were scientists or not.

He'd managed to get surprisingly far into the building without being asked for a form of ID. Rose had explained that most people were checked before entering the building, so it was unlikely that they would get checked again. As long as Jack didn't draw attention to himself, he'd be fine. Something he was never too good at.

"There should be a sign just down the corridor," Rose instructed. Jack saw plates of glass attached to the wall at the end of the corridor, and sped up to get to them. He glanced over the sign looking for directions to the genetic laboratory.

"It says to go right," Jack said.

"That's it, then about halfway down the corridor should be another one on the left. Go down that and it's just down there," Jack followed the instructions, and sure enough, he soon found himself outside a set of double doors with a sign on saying 'genetic laboratory'.

"I'm here."

"Ok, use your physic paper to get in, but remember don't use it on anyone in there," she said.

"Yeah, I know," he waved the physic paper over the sensor by the door and waited for the lock to click open, and walked through the doors.

As he walked in, he saw people all around him rushing around, with clipboards or PDAs, talking into headsets. There were desks with computers analysing data from the DNA samples one other desks. He could see test tubes of blood and beakers of various solutions. Scientists were performing experiments around the room. "Bit crowded, isn't it?" Jack said.

"It would be," Rose agreed. Jack looked around for a second longer, then headed into the room.

"Captain Jack Harkness!" he spun round to see Yvonne walking up to him. "What a surprise to see you here."

"Well," Jack said, turning off the headset connecting him to Rose and trying to think of an excuse, "I heard you caught a live alien. Couldn't resist the urge to come and have a look," he said casually.

"You made it here quickly from Cardiff," she said suspiciously.

"We found a teleport," he quickly lied, "thought it was a good time to test it out." Yvonne looked suspicious for a moment, then nodded and began to lead Jack away.

"So how much do you know about this alien?" she asked as they walked through the lab.

"Nothing, other than he's alive."

"You know it's a he as well then?"

"Oh... Yeah." Yvonne led him to a table with what Jack recognised as the Doctor's belongings on it.

"We found these on his person," she explained, "but, to be honest, we don't know what most of them are." Jack looked over the various items on the table, some he recognised, some he didn't. "We questioned him on what some of them were, but he didn't say much," she picked up the sonic screwdriver. "This, he said, was a 'sonic screwdriver'. He expects us to believe that?" she asked with a laugh.

"What else did you ask him?" Jack asked.

"What the blue box is and how to get into it. But he wouldn't talk."

"What did he say?"

"First he asked about Rose, and I stupidly said that she escaped. We could have used her as blackmail and threatened to hurt her if he didn't talk, 'cause what we're doing to him now sure isn't working."

"And what are you doing now?" Jack asked nervously.

"His body is much stronger than a human's. If we can find out why, we can improve the human race. But first we need to find what extremes he can survive at."

"When you say extremes, what exactly do you mean?" Jack asked, fearing he already knew the answer.

"Environmental extremes. Temperature, gravity, air pressure... He can survive in a vacuum, but I think we may have left him in there too long... He nearly suffocated." Jack stared at her with wide eyes. "Don't look at me like that. We need to know this. We've told him that we'll stop if he tells us what we want, but he refuses."

"You're torturing him," Jack said darkly.

"It is required. Besides, he stole from us. He deserves punishment. Would you like to see the results?" Before Jack could answer, she was already leading him through the lab.

xxx

Yvonne led Jack into a small room, which had a large window on one wall looking into another room with completely white walls. "That's an environment simulator, it can produce almost anything we want it to." Jack glanced into the room, knowing how powerful it could be. He then looked across at the desks against the walls, with machines and papers scattered across them. Yvonne walked up to one of the computers and typed something on the keyboard. The screen flashed on, and Jack slowly walked up next to her as she continued working. A program started up, which displayed information on the simulators status. Yvonne typed something else in, and more boxes flashed up. "We monitored his body. This is his heart rate, he has two hearts by the way, his body temperature, brain waves and blood pressure." She typed something else, and waves appeared in the boxes, showing each piece of information as the conditions in the simulator began to change. Jack watched as his heart rate increased and decreased, his body temperature rising and falling.

"Where is he now?" he asked abruptly.

"Don't you want to see the results?" Yvonne asked.

"I've seen enough. Where is he now?" Yvonne rolled her eyes.

"We're testing to see what effect different chemicals have on his body," she answered. "This way." She walked out of the room, and Jack followed her.

xxx

"We're injecting chemicals into him to see the effects," Yvonne explained as they walked through the labs.

"But what if you poison him?" Jack asked angrily, "You don't know anything about him. You could and up killing him!"

"We're monitoring him. We take regular blood samples and check for short-term and long-term effects. I assure you, we're not going to let him die." Jack wanted to tell her right then what he felt, but he knew if he did she'd just get security on him and lock him up.

Soon they came to another door. "He's in here," Yvonne said, as she pushed it open.

The room was similar to the other one, but this time people were at the machines and were going in and out of the room. Jack looked at the window on the wall, and slowly walked towards it.

His eyes widened as he saw the Doctor slumped on the floor, his hands and feet chained to the wall. Surrounding him were scientists, watching and making notes as others injected chemicals into him. He was pale and tired, resigned to it, as if he'd learnt that fighting back just brought more pain and had given up.

"What have you done to him?" Jack asked in a whisper, not taking his eyes off his friend.

"You know what we've done to him," Yvonne said simply. Jack watched as the Doctor winced as another chemical was injected into him.

"Can he see us?" Jack asked quietly, at a loss for what else to say.

"No, this is one way glass," Yvonne answered. Jack stared as the Doctor threw his head back from the latest injection, crying out in pain. On the computer screen, his dual heart rate increased rapidly and his body temperature soared. Moments later, the gently fell and returned to normal. The Doctor gasped, wincing in pain.

"Stop this," Jack said darkly.

"Why?"

"I'm telling you to stop this!" he demanded with such force that Yvonne visibly flinched, a rare thing for her. The room fell silent as the scientists watched her. Slowly, she nodded.

"Take him back to the cell," she said quietly, and they quickly did as they were told. Jack watched as they began to unlock his chains. "Come on," Yvonne said to him, walking out the room. He took one look back at the Doctor, then left the room.

"Now what do we do?" Yvonne asked as Jack met her in the lab.

"Question him again," he answered, "Tell him you'll stop this if he opens his ship." Yvonne nodded, and began to lead him through the lab again.

Xxx

Jack waited impatiently outside the interrogation room. He looked up at the door as Yvonne waked out.

"He still won't talk," she said, "he refuses to give us any information about anything." Jack sighed.

"Let me talk to him," he said.

"Why? What are you going to do?"

"I can be very persuasive when I want to be," he said confidently, "Trust me." Yvonne watched him for a moment, then nodded. "Thanks," Jack said with a grin, then walked into the interrogation room. Yvonne turned down the corridor and went through the door a few metres down. Once inside, she looked up at the screen displaying the footage from the security camera in the interrogation room.

Xxx

The Doctor sighed as he heard the door open for the second time, not even bothering to raise his head to see who was waiting for him.

"Hey doc." His head snapped up suddenly at the sound of his friend's voice.

"Jack!" he gasped in a hoarse voice, grinning at him. "You took your time."

"Oi watch it," Jack warned with a laugh. He walked over to the chair on the opposite side to the table in front of the Doctor.

"Where's Rose? And Martha? Are they ok?" he asked as Jack sat down.

"Yes, they're fine, stop worrying about them." He watched the Doctor for a few moments. He was still as pale as before, and looked just as tired. "How are you feeling?" he asked.

"I'm fine."

"You don't look it."

"I must look worse than I feel then." Jack raised an eyebrow at him.

"I saw what they did to you," he said quietly. The Doctor didn't say anything, he just shifted slightly in his seat.

"I suppose it was you that stopped it," he said. Jack nodded. "Thanks." Jack smiled at him.

"Tell them you're going to open the TARDIS," he said, "I'll be there, we'll quickly go in before they can stop us. The TARDIS will have enough power to leave, right?"

"I don't know," he answered, "with any luck, yes. But we can stay in there, they can't get in." Jack nodded again, and stood up.

"Right then. I'll tell them you've agreed to open the TARDIS. I'll see if I can get your stuff back in the meantime too," Jack said. The Doctor nodded his thanks, and Jack headed for the door.

xxx

Yvonne stared at the screen in surprise.

"He's on his side," she said numbly. "How could I not have noticed? It was obvious!"

"Miss Hartman," one of the guards said and she turned to face him, "shall we arrest him?" She thought for a second, then shook her head.

"No. We may be able to use this to our advantage," she said thoughtfully. "Find out how Torchwood 3 knew that we'd captured and alien, exactly how Jack got here, and exactly what they want with the Doctor." She watched as Jack stood up and headed for the door, and headed for the door herself.

She walked out of the room and down the corridor, and met Jack as he came out of the door to the interrogation room.

"Well?" she asked, and he nodded.

"He said he'll open his ship," Jack answered. She raised her eyebrows.

"Oh? And how did you do that?"

"Just told him that I was the one who stopped what you were doing to him. He seems to trust me. You need to try being nice once in a while," he said with a wink. Yvonne nodded slowly.

"I see. Well, we'll have him taken to his ship then. But first, I want to ask you some things," she began to lead Jack down the corridor. "Firstly, how did Torchwood 3 know we had an alien?"

"Oh, you know… we detected alien tech here and looked through CCTV, and we saw you capture him," Jack answered.

"You know you're meant to leave alien activity in London to this Torchwood."

"We weren't going to interfere. We just wanted to know what it was."

"You seem very protective over him."

"You can't treat people like that!" he said angrily, "even if he did steal something from you. He doesn't deserve torture." For a moment Yvonne didn't answer.

"Well we're not torturing him now," she said finally. Jack sighed.

"Miss Hartman?" they turned to see a young woman standing behind them. Yvonne turned to Jack.

"Excuse me a second," she said, and took the woman to the side. "Well?"

"Um, we contacted Torchwood 3 and… they don't know anything about this. Jack Harkness is there, in Cardiff. They don't know anything about the alien." Yvonne frowned at her, then turned back to Jack, then back to her.

"Thank you… Danielle, is it?" Danielle nodded, "Thank you Danielle," Yvonne repeated, then turned back to Jack with a smile.

"Everything ok?" he asked.

"Oh yes, fine," Yvonne answered, "just one more question: who are you?" He frowned at her intensely.

"What?" he asked in confusion.

"Captain Jack Harkness," she said thoughtfully, "yeah right. Guards," she looked behind him and he spun round to see a pair of guards behind him, "take him away." The two guards advanced on him, grabbing his arms before he could get away.

"No!" he shouted as he struggled, but it was no use. The guards dragged him down the corridor, and he threw one last look at Yvonne, who was smiling smugly at him, before he was dragged away.