A note to avoid confusion: The first snippet is alternate dialogue during Last of the Time Lords after Lucy shoots the Master. The second snippet explains itself, really. The third snippet is a prologue of sorts to the first snippet. The fourth snippet is a line of dialogue from a conversation set sometime after the second snippet. The fifth snippet is set sometime after The End of Time.
"No, no! Don't die! I love you, don't die, live, we can start a new life together, travelling through galaxies like we always talked about…" He was crying, hardly registering what he was saying, what he was doing when there was nothing he could do.
"You went all on your own, though," the Master panted, his body struggling to keep his hearts pumping, "And I'll never say I forgive you for that, because if you wander those galaxies for a thousand years feeling guilty, I'll be glad to have made you feel just a tiny amount of my pain! You left!"
And the Doctor bowed his head, tears running down his face, because there was nothing he could say and he knew it.
"Hey Doctor, have you ever had a girlfriend? Wait, no, don't tell me, a boyfriend?"
"You just assume he's gay?" Rory spluttered at Amy.
"Well, Pond, Rory," the Doctor said loudly over the comment Amy was making, "Let's go to this nice planet I've always wanted to visit."
When he pulled the lever, she realized just how stupid it was for him to take them to the planet he and the Master had been planning to visit first, all those eons ago on Gallifrey.
Time seemed to slow down and the world was mute as the shot hit the Master. The Doctor was aware that he yelled the Master's name, his real name that he had cast off years ago, not his pseudo-powerful nickname. He was also aware that in a moment of vulnerability the Master whispered the Doctor's real name, not the name he had taken to make him feel like he was a helper of worlds and didn't just bring destruction wherever he went. For a moment, the Master's face was blank and innocent, and when that gaze focused on him he realized that the Master had never stopped loving him.
He also realized that he had never stopped loving the Master.
"You know, Pond, I got him killed. It was my fault; it's always been my fault. I left him, I drove him insane, I got him killed. He died saving me. I don't deserve that."
"And running. A whole lot of running."
In his dream, they run, but they run together, all throughout the universe. And they can kiss or hold hands wherever they like, and they can always be together.
They can always be happy.
He wakes up crying.