Honestly, I think this story is terrible. It doesn't flow right, and there are extra things that I just don't really feel like they belong, but, I tried. I hope it isn't TOO terrible.
By the way, this completely ignores the Metacrisis Doctor and the Daleks and Rose coming back and the Doctor Donna and all that.
The other Doctor that just appeared screamed and twisted around. "What's happening? I wonder if we'll get back. Yes, one day... Aaagh! I've reversed the polarity of the neutron flow."
"The Flesh is struggling to cope with our past regenerations. Hold on!" the real Doctor said as they all watched the copy.
"Would you like a jelly baby?" the other Doctor said in a deep voice, holding his arm out. In his regular voice; "Why? Why?! Why?!"
"Why? Why what?" the real Doctor asked.
"Hello, I'm the Doctor," he said in a different voice. Hiis face suddenly twisted in pain. "If it's my last chance to say it… Rose Tyler…" Then, when he got back to his normal voice: "No, let it go! We've moved on!" He lunged at the Doctor. Amy started forward, but was pulled back.
"Hold on, hold on, you can stabilise!"
The other Doctor grabbed at the real Doctor's jacket. "I've reversed the jelly baby of the neutron flow… Would you like a ROSE TYLER I LOVE YOU!" the other Doctor collapsed in the real Doctor's arms, crying. "Rose… Rose… I… love…" He looked up at the real Doctor. His face was white and liquid-y, and his eyes were bloodshot.
"It's going to be okay…" the real Doctor mumbled. The other Doctor leaned into the real Doctor's chest for a few moments, and when he put his face back up, it was identical to the real Doctor's again, with the addition of tears trailing down it.
Suddenly, something started pounding on the door. Immediately, the other Doctor jumped up, acting cheerful despite the tears.
However, the other Doctor was quieter, sadder. No one but the real Doctor had noticed, or else they would have known that the Doctors switched shoes.
"Doctor," Amy said to the other Doctor, although she thought it was the real Doctor. "Who is Rose Tyler?"
The other Doctor looked down at his shoes, which of course were the ones the real Doctor had gotten after the original got stuck in acid. "She is… not important."
"You—I mean, the copy of you—" The other Doctor flinched, but not enough for Amy to see. "—said that you loved her. I think that is important."
"Now is not the time, Amy," the other Doctor said, straightening his bowtie. "We need to get back to work."
"But you love a girl!" Amy said, tugging on his sleeve. "I need to know about her! I won't just hand my raggedy man to anyone."
"Okay, fine. She was the first face I ever saw with the two faces I had before this one. Now she lives in an alternate reality and I can never see her again." His voice cracked on the last few words, and tears sprung in his eyes.
"Oh," Amy said. "I'm sorry." She went off. Rory was still missing.
0o0o0
"Amy, we swapped shoes. I'm the Doctor."
"And I'm the Flesh."
"You can't be." Amy looked at the other Doctor. "You're the real him."
"No, I'm not," the other Doctor replied. "And I haven't been all along. Even before I told you about Rose Tyler."
"What?" Amy said in disbelief.
"I'm the original Doctor, Amy," the real Doctor said to her. "We had to know if we were truly the same. It was important, vital, we learn about The Flesh. And we could only do that through your eyes."
"We are still not the same, though," the other Doctor said, his eyes clouded with sadness. "He has gotten over her over time, but I didn't have that time. I feel like I lost her hours ago, not years ago."
"Rose?" Amy asked. The other Doctor nodded. Amy ran up to him and hugged him.
"Push, Amy, but only when she tells you to," the other Doctor whispered in her ear.
The other Jennifer banged on the door. "Amy, come on!" Rory yelled. Amy obeyed.
"Well, my death arrives, I suppose," the other Doctor said.
"No," the real Doctor said. "I need to give you something." He took something out of his bigger-on-the-inside pocket and tossed the other Doctor the object. He tossed him his sonic screwdriver as well.
Being the only one outside of the TARDIS besides his ganger, the real Doctor exchanged a nod with his ganger and went inside the TARDIS. It started to dematerialize.
Now that the other Doctor was alone, the other Jennifer finally burst through the door, and the other Doctor pointed the sonic screwdriver at her. "Allons-y and geronimo!" He pushed a button, and the other Jennifer burst. At the same time, the other Doctor pressed the button on the object in his hand, and he disappeared.
0o0o0
Somewhere far, far, FAR away, farther than anyone could get by staying in one universe, a woman was taking a walk on her own, looking at the ground beneath her boot-covered feet. She couldn't ever see the sky, because it was always covered with—
Her thoughts about the sky were interrupted as a man wearing a bowtie appeared in front of her. He just— appeared! Out of thin air! The woman hadn't seen something like that since—
"Whew, just barely escaped that one." The man looked at her, and his eyes immediately softened. "Rose Tyler…"
"Who are you?" Rose asked.
"It's me, I'm the Doctor… well… actually… I'm the Doctor's ganger… Gangers are—"
"I know what gangers are," Rose said bitterly. "The way they're treated is awful. Every day, gangers die, and no one cares." Suddenly, tears formed in her eyes. "Doctor…" She flung her arms around him.
All of his fears of being turned away from the love of his life disappeared. "I regenerated again."
"I see that." Tears of joy were running down her face. "But I don't care. I don't care if you're a ganger, either." She pulled away from the hug, looking at him up and down.
"Do you still… do you still…" he stopped, realizing he couldn't finished the sentence, and tried something else
"I love you," the other Doctor said. "I love you so much. Even though I am not the real Doctor—"
"You are the real Doctor, and I love you, too. I always have." As soon as she said that, the other Doctor pulled her into a chaste kiss.
"Thank you," the other Doctor whispered.
0o0o0
Back in the TARDIS, the real Doctor smiled. He had gotten over Rose (mostly, at least, his metaphorical bandage was still pretty tight on the metaphorical wound), but his ganger hadn't. Now, his ganger had Rose and Rose had his ganger, and they were both happy.