He had been traveling alone for too long. Riversong always adviced against it, but he felt he deserved it. Perhaps he was punishing himself, who knew?
The lack of friendly faces, of companions, of allies, was beginning to affect him. He needed to be strong, however. Whenever he traveled with someone, he ended up hurting them.
Too many people had lost their lives because of him, so many friends lost everything they held dear after meeting him, after traveling with him.
He was sick of it.
They were better off without him: Amy and Rory, Martha, Rose, everyone.
It was hard, harder than anything he had ever done before. Traveling alone hurt. But in the end, it was worth it.
The Doctor and his TARDIS, moving back and forth the entire space and time without anyone by their side, with no one to distract him from his own thoughts and feelings.
Life was getting grim, dark, intense. He needed someone to distract him, to lose focus on his obsessions.
But he needed to stay alone. He needed to save potential companions from the heartbreak and the suffering they'd encounter by his side.
Traveling alone was painful, but it was the right thing to do. And he'd continue doing it as long as he could.