At the very end of Time, well after the failure of Utopia, there is a box. It is small and would be of no consequence if not for the fact that it is the last occupied dwelling in the galaxy. Perhaps the universe.

"Getting a bit late, isn't it?" The speaker is thin and blonde. He was once a madman, but sanity and insanity don't apply to such as these. Not in the end days.
"How would you be able to tell if it was?" responds his dark-haired companion wryly. "It's been dark out for ten thousand years now."
"And if you had the slightest clue how to maintain a TARDIS properly we wouldn't be here, now would we." The man who was the Master long ago chuckles. "Not that it matters, really. We're old enough now that I'm rather looking forward to it."
The Doctor smiles. "Remember the Toclafane? It was fun to see them again."
"It was, yes.." The Master looks out at the sky. "I do believe the last star just went out. Shall we?"
The Doctor nods and takes the Master's hand, and together they step outside for the last time.
There is a sound of wings, It is the last sound ever heard this time around.

Heaven has red grass and silver trees. The sky is orange. And two men leave their bigger-on-the-inside house to watch the sunset every day. It is quiet in the Master's head, and the Doctor can finally stop running. It's a good way for the long story to end.