My Little Pony: Friendship is Magic - Image #228,541

@Ric Tesla
The Doctor is over 900 years old and is practically immortal, he's the last of his kind in the universe. (he's checked)
He's been almost everywhere and seen almost everything.
He travels alone because it's safer that way, (for others, he's not concerned with his own safety anymore) but he can't stand the loneliness.
There are times, when the loneliness gets too bad and he DOES let others travel with him, but they can never stay for long; he's too protective of them.
He has thousands, maybe MILLIONS of friends all across time and space but he can NEVER be with them for fear that his mere presence will put them in harms way, he can't afford to love, because they would whither and die and he would be forever young.
This is one of those moments where he has just left one of his dear friends behind forever and he has to travel alone.

Tl;DR?
he gets friends
he leaves friends
he gets friends
he leaves friends
Rinse repeat.