Note from Whovianpower: Just in case there is any confusion, this is where each character is in their timelines.

River Song: After "The Wedding of River Song"

Amy, Rory, and the 11th Doctor: After "The Power of Three" and before "The Angels Take Manhattan"

Donna and the 10th Doctor: After "Midnight" and before "Turn Left"

Rose and the 9th Doctor: After "Father's Day" and before "The Empty Child/The Doctor Dances"

Jack Harkness: After "Utopia/The Sound of Drums/The Last of the Timelords" and before "The Stolen Earth/The Journey's End"

There. Hopefully that clears up any confusion. Thank you and enjoy the story. Reviews are appreciated. I don't own anything.

The Doctor and River just stood together, locked in embrace, as Rory tried to process that the woman-Donna- had seen River dead.
River died. His daughter died for the Doctor. By the sound of it, it had been before her time. Rory wasn't sure he could forgive the Doctor for that. He couldn't speak for Amy. She's a wild card, that one, but he was sure that Amy wouldn't be happy to hear of her daughter's death.
Loud voices outside the locked door brought River and the Doctor apart. They moved as if nothing happened, and the news of River's future death circumstances had not just been revealed.
"All right," the Doctor said. "We've got work to do." He turned to Donna. "Donna, come here, and use this electromagnetic locking system of River's to enforce the closed door." He thought for a moment. "I- er, I mean- the Doctor has shown you how to do it, right?" Donna nodded weakly. The Doctor herded her to her feet. "Well, off you go!" the Doctor said, pressing a strange gizmo into her hands. He turned to Rory, and handed him the Sonic Screwdriver.
"What do I do with this?" Rory asked, grasping the device. The Doctor pointed to Donna.
"Go make the locking system stronger." The Doctor instructed. "Setting 2634B."
Rory did as he was told.
The Doctor and River headed off to the other side of the room. Rory noticed their glowsticks light up a computer that he hadn't noticed before.
Rory found Donna pressing the gizmo to the door, right above the handle. She did something, and there was a snap as it latched into place. A small light on the top lit up.
Rory set the Sonic Screwdriver to the right setting, and turned it on. Donna watched the device intently.
"What's that?" she asked.
"The Doctor's Sonic Screwdriver."
"The Doctor? He's here?" Rory looked at her strangely.
"He's been here the whole time," Rory told her. "He's that annoying bloke with the stupid bowtie." Donna stared at Rory like he had just grown a second head. She then glanced behind her, probably at the Doctor, and then back at the Sonic.
"That isn't the Doctor." Donna said. "The Doctor looks completely different." Rory's head shot up suddenly as he realized why Donna didn't recognized him, if she really even did know the Doctor.
"Oh, I get it now," Rory exclaimed. Donna raised an eyebrow as Rory spoke. "The Doctor is an alien."
"I know that," Donna interrupted. "He's from Gallipawn, right?"
"Gallifrey," Rory corrected. "He's an alien, a Timelord. Timelords have a special power. When a Timelord dies, their body repairs itself, it changes. His entire body changes. He gets a new face and a new body." He gestured towards the two people, huddled together in front of a computer. "He told us after River was born."
They were silent for a moment. Surprisingly, Donna seemed to accept this fact very easily.
"River… is she your daughter?"
"Yeh," Rory said. "She's my daughter."
"I'm sorry."
"Yeh," A tear slithered down Rory's face. The Doctor was the cause of his daughter's death, and that was killing him, even though his daughter was alive and well across the dark room.

Just when Amy thought she would go insane, the Doctor broke the silence. His eyes were still brimmed with red, but he stood up like a man late for work, and hurried to the control panel. He began to mutter indistinctively.
Amy stood up slowly. She felt herself starting to sweat from the heat. She took a hair tie off her wrist and started putting her hair up.
"What?" she asked as she pulled her hair tight. The man who calls himself the Doctor didn't turn to look at her.
"I'm gonna blow the place." Amy's eyes widened.
"What?" she cried, hurrying over next to him. "But we're still inside!"
"Don't be stupid, I know! I'm gonna beam us to the TARDIS," he said to her as if it were the most obvious thing in the entire world. Amy narrowed her eyes.
"Who are you?" she demanded.
"I'm the Doctor," the Doctor snapped. Amy threw her arms in the air.
"You are not the Doctor!" She cried.
"Yes I am!" he turned to stare her in the face. "Who are you?"
"Amy Pond! You know that already!" The Doctor rolled his eyes.
"To me!" he said in annoyance, pointing to himself. "Who are you to the Doctor?"
"He's my best friend!" Amy told him angrily. "I travel with him. I think I know what my best friend looks like!" The Doctor glared at her.
"You don't know what he looks like in the past!" He snapped as he pressed a button.
"What are you-" Amy trailed off, lost in thought for a moment. She suddenly slapped herself on the forehead. "Oh my G-d!" she cried. "It's been staring me in the face!" She had learned this when River was born! "He's regenerated!" The Doctor glanced at her.
"Yeh, you travel with a future version of me." He confirmed. "You know, unless I've lost my memory, which is highly unlikely." He stepped away from her and pressed a button farther down the control panel.
"So… you are my best friend before I knew you?"
"Ya," the Doctor answered. "But you aren't my best friend. I don't know you." He was silent.
Amy was too, since her heart suddenly felt heavy. She spoke with a shaking voice.
"So what's the plan?" she asked.
"I'm gonna set the boiler room into overdrive, causing radiation to flood this place. The gas pipes will burst, and the only thing I'll need to do then, is strike a match." He glanced at her and flashed a momentary small smile. "Charles Dickens gave me that idea last Christmas. The place will blow instantly, but the TARDIS will bring us in before we become fish and chips."
"Nice!" Amy shouted. "How long will that take?"
"All I need to do is press this button!"
Suddenly, there was a small explosion. Amy screamed, jumping backwards. The Doctor scrambled around, trying to do damage control. His cries of dismay claimed that it was too late. The console was being licked by flames.
The Doctor grabbed a leather jacket that Amy hadn't noticed until then off the floor besides the console, and joined her a safe distance away from the fire.
"What's happened?" Amy cried. The Doctor's eyes darted around observing the scene.
"It's the Daleks!" he shouted in anger. "They've figured it out. They've sent a heat pulse to melt the controls!"
Amy watched in dismay as the fire burned the controls into ashes.

The Doctor stared at Rose for a very long moment. He felt Jack's eyes on him, but he didn't care. The Doctor felt his hearts well up like balloons, and a tear slither down his face. He approached Rose, and reached out. He stroked the side of her face, and then pulled his hand away, unable to believe that Rose was really there.
Her breathing was shallow, and her bruises were a deep purple. The Doctor touched her forehead lightly, but she jerked away with a small whimper. She didn't wake.
He finally spoke to Jack, but didn't take his eyes off Rose, in fear that the moment he looked away, she would be gone.
"When did you find her?" He asked.
"I sent that distress signal out a month ago, the day I found her." He replied in a sad tone. "She's been sleeping the entire time."
"A month," The Doctor whispered, getting to his knees. "She's been in a coma for a month." He bit his lip as he noticed a large bandage wrapped around her stomach. "What's happened there?"
"There was a burn mark." Jack told him. "Looked like it was caused by the weapon of a-"
"Dalek," The Doctor whispered. "She had been shot by a Dalek. She shouldn't be alive."
"I know," Jack whispered.
The Doctor felt more tears streaming down his face.
"But she's alive," he whispered. "If anyone could survive a Dalek, it's her."
"Doctor, can you wake her up?" Jack asked. The Doctor swallowed a lump in his throat. He knew the truth. He didn't know if he could.
Jack got the message, even though the Doctor hadn't said a thing. The Doctor stroked Rose's hair again, with mixed emotions swirling inside of him.
The Doctor sniffed, then stood up, taking his eyes off Rose for the first time.
"What do we have here?" He asked. "What supplies do we have?" Jack nodded, and hurried out the door. He returned in under a minute with the med kit the Doctor saw earlier.
"Modern or future?" he asked. Jack smiled and opened it.
"How about both?"
The Doctor looked over the medical supplies. Stethoscope, decongestion medicine, thermometer, aspirin pills (he shuddered at that one. It kills him instantly). He took the pills and threw them behind him. He heard them roll away on the wooden floor. There were also some medicines from the future, cures for diseases that didn't exist yet. Those were useless.
The Doctor pulled out the stethoscope and put it on. He placed the stethoscope over her heart. Rose winced at his touch, but relaxed at after a moment. The Doctor listened, and felt his heartbeats quicken. Rose's heart was working overtime, as it had been for a month, struggling to keep her alive.
According to the thermometer, she was burning with fever. The Doctor glanced at the supplies at his disposal. They were all useless.
He was about to give up on what he had when he notice something.
"Jack, what's that?" the Doctor asked, pointing to a jar in the kit. Jack, who had placed the kit on the floor and was standing in the doorway, approached quickly. The Doctor pointed to a little flap sewn into the back of the kit where the aspirin used to be.
"I'm not sure," Jack replied. "I never used the aspirin."
"Jack, what century is this box from," the Doctor questioned. "Now, or 51rst?"
"51rst," Jack said. "Does it matter?"
"Med kits may not always have what you need," The Doctor said. "But there's a way to get what you need." He opened the flap, and exposed a dark hole, just big enough to put fingers through. He reached in, felt around for a second, then pulled out a long narrow tube, filled with a golden light.
"Spatio-Temporal Hyperlink!" he cried happily. Jack opened his mouth, but the Doctor cut him off. "Yes, I know it isn't a real term. I just didn't want to say 'Magic Door'."
"What is that?" Jack asked pointing to the tube. The Doctor smiled.
"Think, the first time we met, what was floating around in your ship?"
"Nano-genes!" Jack cried. The Doctor took out his Sonic Screwdriver, and quickly scanned Jack.
"I just show Nano-genes what a healthy human looks like, take out the immortality from the mix, and send it to the Nano-genes!" The Doctor did what he explained, then soniced the Nano-genes. They shimmered with a bright golden light, and the Doctor jumped to his feet.
"Brilliant!" he cried. To Jack, he said "Are you ready?" Jack nodded. "Allons-y!" the Doctor cried, popping the lid off the jar. The Nano-genes streamed out, and surrounded Rose. The Doctor stepped back as the Nano-genes went to work.
The Nano-genes manifested around Rose physical injuries. When they cleared, the bruise or cut would be gone. Within a few minutes, the Nano-genes left a healthy looking Rose, and disappeared into the air.
The Doctor hurried forward, grabbing the stethoscope from the medical kit and putting it on. He got to his knees again, and put it to Rose's chest. She didn't wince this time. Relief showed on his face as he listened the strong, steady beat of Rose's heart. Her breathing returned to normal, and so did her temperature as the fever died.
The Doctor glanced up at Jack. "She's gonna be alright." He cried happily. His hearts nearly stopped as he heard a small cough and a gasp coming from Rose. He turned in time to see her rise up to a sitting position, glancing around groggily. When her eyes fell on the Doctor, Rose flinched, and pushed herself to the edge of the bed against the wall.
What she said to him next nearly stopped his hearts for good.
"Who are you? Where's the Doctor?"