A/N: Well, this is new for me. I guess I got a moment of inspiration from this week's episode of 'Doctor Who.' So this episode takes place straight after the events of 'A Town Called Mercy,' so nothing of 'The Power of Three' will be mentioned in this for obvious reasons. There's going to be a lot of Doctor!Whump and most of the companions will be harmed both mentally and physically throughout this story. Read with caution, there will be some dark themes including some Dark!Doctor. Nonetheless, I hope you enjoy and please be sure to review!

This fic was slightly edited on 26/11/13

Chapter 1

Amelia Pond - fiery red head and current companion of the Doctor – leant her full body weight on the silver railings that outlined the TARDIS console room. She stared blankly at the main console unable to make a sound, she couldn't bring herself to. She was the girl who waited, but now she was growing impatient or no… maybe it wasn't impatience. Maybe it was worry. She blinked once and then twice, but the tears were already flowing. She had no time to stop. She just stared.

Rory Williams - the last centurion who had almost given in to having the Doctor constantly calling him Pond – stood next to his wife. He knew how she must have been feeling and even though he knew it would be easy to fall into a state of disbelief, the inner nurse in him said differently.

He really should have seen the signs; after all, he'd spent his entire career doing so. Being ever vigilant. Maybe it was because the Doctor was a Time Lord, maybe he just hadn't considered the possibility that he could even... Still, the change in personality, the way that he had gone against his entire system to put someone to justice. He had a darkness lurking inside of him and up until then, Rory hadn't realised just how dark it was. He had understood the Doctor's reasoning, of course he had. Save an entire town from the Gunslinger by sacrificing one awful war criminal. Not hard.

But then the Doctor had pulled the gun and it had all fallen apart. Rory had seen it in Amy's eyes first. She'd realised what being alone did to the Doctor. He'd told them the stories, and maybe they should have listened harder, because what he had done in his past wasn't pretty. He'd sacrificed so much for the greater good. The Doctor told the two companions about Jex and what he had said before he died. The story of how his soul would carry every single person he had wronged up a mountain. The Doctor had recited the story with such distaste… it didn't take a genius to figure out he was thinking about himself. Twelve hundred years of sacrifice, twelve hundred years of mercy. And then just five seconds with a war criminal and all that mercy had evaporated. As though it had never existed.

Suddenly, the TARDIS made another unhealthy groan which effectively pulled both Rory and Amy out of their shared memories. They both glanced up at the same time as the TARDIS groaned again. It wasn't the usual groan that the couple were used to, no; this was much, much worse. The Doctor and the TARDIS were connected and the couple really didn't want to go into details on how, but those two had been together for just under a millennia and that was enough for the two companions to believe it. Now the TARDIS could feel everything the Doctor felt and in return the Doctor could feel the TARDIS. The couple winced as the next groan was accompanied by a noise that reverberated from somewhere deep within the TARDIS. A loud cough coupled with a low, tired moan. Somewhere in the TARDIS the Doctor lay incapacitated and Amy and Rory could do nothing about it.

"This isn't right," Rory said after what felt like an eternity of silence. "We need to do something."

"Like what?" Amy asked tiredly, she'd almost given up with fighting. She just wanted all of this to end so she could get her raggedy Doctor back, "We tried, Rory, but what did he do? What did that stupid, stupid loon do?" she gritted her teeth and sucked in a pained breath, "He went off, claiming he could take care of himself." She shook her head in distaste as her eyes fell back to the floor, "But he can't. And what's worse is even now the TARDIS is hiding him or whatever," she waved a dismissive hand and shook her head. "Like we'd only make things worse."

"He was burning up, Amy." Rory tried to argue, but he knew it was useless, "I… I should have seen it. He just wasn't acting himself back in Mercy. Like he'd… I don't know."

"He knew the rules," Amy said carefully. "He knew what he was doing was wrong and I was so afraid he wasn't going to stop."

"We have to help him, I don't know how but I can't just stand here and do nothing!" Rory roared as he moved away from the rails and walked towards the staircase.

Amy watched him disappear as a few more tears dribbled from her eyes and down her cheek, "Rory!" she called weakly before letting out a stifled sob. She rolled her eyes at her stupid faced husband as he made his way down the hallway.

"The TARDIS won't show you the way, she never does…"

Amy couldn't get the images of the day previously out of her head. She and Rory had resolved to go home, but just minutes after they had boarded the TARDIS, they noticed the Doctor wasn't acting like himself. He stumbled slightly as he strode around the console and his breathing seemed faster and harder than usual. Amy had originally wondered if the Doctor's outburst in their latest adventure had taken a toll on him, and maybe it had, but even when they were in Mercy he'd been leaning against things more often, rubbing at his head… yawning. Whatever tiredness had overcome him had done wonders for his personality. He'd been so angry with Jex, even angrier than he had been with the Daleks back in Winston Churchill's bunker. Amy couldn't disagree with his reasons for hating Jex, but that day the Doctor's dark side shone through. He did such a good job to hide it most of the time, but the way it had so easily slipped through his defences…

Mercy.

The Doctor's dark side had no mercy.

Rory had realised that the Doctor was feverish. He had been flushed and panting and although Rory had to more or less wrestle the Time Lord to get a feel of his forehead, he had felt the Doctor's skin and knew something wasn't right. From the books Rory had read in the TARDIS library, a Time Lord's normal temperature was significantly cooler than a Human's. He guessed it was why the Doctor's skin always felt so cold compared to his and maybe also why he seemed unaffected by extreme climates.

"It's nothing!" The Doctor had warded off the concern in his companions fairly easily, but after he stumbled yet again, he knew that he had to say something. "Well okay, maybe it's something, but nothing I can't handle." Then he'd flashed that goofy grin and set in the co-ordinates for Earth. After that, the couple watched as the Doctor tried to hide any signs of illness. Any coughs were hidden with a clear of the throat and any weakness of the knees was hidden when he relied on the TARDIS console to keep him standing.

"Maybe we don't have to leave just yet," Rory had said after speaking with Amy. The couple agreed it was for the best. Even if their friends were beginning to take notice of the small changes in their appearance, it didn't come anywhere near in the priorities list when it came to the Doctor. Amy's raggedy Doctor, the man she had waited on for twelve years, the man she had dedicated her life to. That mad, daft old idiot alien whom she always got in trouble with and always, always had each other's back.

Amy absentmindedly clicked her tongue against the back of her teeth as she waited for her husband to return. "Gotcha," she whispered.

After that, events had transpired rather quickly. After a lot of persuasion from Amy and Rory, the Doctor had finally agreed to rest for a short while, still convinced he could take care of himself. He hadn't even told the couple where his room was or even if he had a room and since then, the Doctor hadn't been seen, only heard.

Amy turned her attention back to the TARDIS as it groaned once more. That one sounded particularly bad. Whatever was wrong with the Doctor, it wasn't getting any better, if anything, it seemed as though he was getting worse.

"I hate him," Rory muttered as he returned from the hallway. "I kept hearing him, but it's like one of those nightmares where you keep running but you never actually go anywhere." He groaned in frustration before moving back towards the TARDIS, "And fat lot of good you are," he scolded the console, "can't you see that the Doctor's sick?"

The TARDIS only groaned louder in response.

Amy shuddered, "I… I think he's gotten worse."

Rory rolled his shoulders, "Yeah, I expect so."

"What if… I don't know, what if the TARDIS can't help it?" Amy said as she looked back to the console, "I mean if the TARDIS can feel whatever is wrong with the Doctor and the Doctor could barely…" she cut herself off, she didn't like pointing out weakness in the Doctor, it made him seem too human for comfort. Instead she carried on, leaving out any mentions of his growing illness, "I mean, what if the TARDIS is just too weak to help?"

Rory considered it for a moment before he shrugged, "It doesn't matter, we can't get to him so-" suddenly, a shrill ring of a phone cut him off abruptly. Rory frowned, "Is that… is that a phone?"

Amy smirked, thinking back to the first time she had heard it too, "Well we are in a phone box Rory."

Rory shook his head, "No, it's not coming from the console."

Amy's brow knitted together as she listened out for the ring as well. Rory was right, not only was the pitch of the ring too digital for the TARDIS console, but it was emanating somewhere underneath.

Amy and Rory moved together beneath the opaque floors of the TARDIS console room and down towards its lower deck. They walked around all the wiring, fiddling with the Doctor's swing, but the noise wasn't coming from there.

"There!" Amy said suddenly as she turned to see the small tool box the Doctor had used back when the Dream Lord had taken over their minds. Rory moved over to it and groaned in frustration, "It needs a key."

"No it doesn't," Amy snapped as she slapped her right palm firmly against the box. Low and behold, not seconds after, the box fell open, spewing a spanner and a kitchen whisk onto the floor. The ringing got louder as the box opened and with a bit of rummaging, Rory pulled out a sleek mobile phone that was only a few years out dated from the ones in 2012.

Rory flipped open the phone and stared at the name on the screen, "Martha Jones? Who's that?"

"Who cares, maybe they can help!" Amy said, suddenly filled with hope. Quickly, she snatched the phone from out of Rory's grip and answered the device, pressing it to her ear. "Hello?"

"Doctor?" The voice wavered a little, unsure of Amy's gender through the rough connection.

Amy froze for a moment. Could she trust a person on the line of a phone that had been locked away and apparently forgotten? "No." Amy said quickly, pursing her lips. After a moment's silence on the other end, Amy quickly carried on, "I mean… no I'm not the Doctor, I'm Amy."

"Look, I'm sorry, but I need to talk to the Doctor, it's urgent. Is he with you?"

"Yes," Amy said warily, "but…" suddenly, her throat closed up, she didn't know what to say.

Rory sensed Amy's lack of voice and quickly grabbed the mobile from her, "Sorry but-"

The voice quickly picked up again, "Doctor?"

Rory grimaced, "Also not the Doctor, sorry. He can't really come to the phone right now."

"Whatever he's doing, it can wait, trust me. Just tell him it's Martha Jones, tell him that-"

"No, I mean we can't give him the phone, we don't know where he is."

There was a brief pause on the other end.

Amy and Rory shared a quick glance when suddenly the voice picked up again, "But you said he was with you."

"Yes, but it doesn't mean we know where he is." Rory let out a sigh, "Look, it's complicated and I can't explain, but the Doctor can't help anyone right now, he's not really himself."

"What's wrong with him?" Suddenly the voice was much more urgent, and very worried. Whoever Martha Jones was, she knew the Doctor personally, Rory knew that for sure. "Is he okay?"

"Look, can I call you back? I really need to sort this-"

"Oh God, sure. Look, I don't know what's wrong with him, but please, you have to tell him that Earth is in danger and we could really use his help."

"Yes, but I don't think you understand, the Doctor can't-"

But the phone line had already gone dead. Rory paused briefly to stare at the mobile before he slipped it into his jacket pocket.

"What?" Amy asked stubbornly, "Rory, what?"

Rory took a deep breath before looking into his wife's eyes with a grave gaze, "Things just got a lot more complicated."