He wanted to do one last thing for Donna, one last thing to try to ensure that she had a happy life on Earth.
He flew the TARDIS into the far future, to the one place he really didn't want to see again. He landed at the transport point where all the people from the Library stopped at before they were sent to their new homes.
He searched through the crowd of people and felt Donna's memories flash with recognition when he saw a dark haired man.
The dark haired man stuttered more than ever when he saw the inside of the TARDIS. He stopped when he was told exactly where he was going and what he could do when he got there.
The Doctor created a false history for the dark haired man and called in some favours to get him a job in IT and a flat in Chiswick.
He landed the TARDIS just down the street from the pub he remembered that Donna went to. He walked with the dark haired man until they got inside, but then went over to sit at the other side of the room.
The Doctor saw Donna bump into the dark haired man as she went to order the next round. He saw the dark haired man introduce himself as Lee, though he stammered quite a bit as he did so. The Doctor then got up and left.
He flew the TARDIS to the not to distant future.
He saw Donna and Lee come out of the church, smiling while their friends threw confetti. He smiled.
He flew a little further.
He slipped on a white coat as he went into the hospital. He strolled into the Maternity Ward and watched from a distance as Donna and Lee cooed over their new baby boy. As he left he heard Donna say,
"Sweetheart, what do you think of the name John?"
The Doctor smiled and knew he had done something good.