It began with guilt.
He killed all of them, he killed all of his own. Two races exterminated in less than the blink of an eye. The Doctor skips along through the when and the stars, running to something other than the now empty parts of the sky he came from. He couldn't face what he used to be, the Doctor had to evolve.
It changed because of innocence.
The victory, finally. It felt empty and unsatisfying for being so, well, victorious. He couldn't take all of the credit of course. Rose Tyler resurrected the thing, protected it and was it's executioner. She held back the tide of rage and fear the Doctor could have rained down upon the last lone Dalek, but the look in her eye as they faced off ... he didn't have much of a choice facing that look. The Doctor's hand was stayed and the last of the Daleks was killed by a child.
It ended with something in between.
At her hand, again. He was the one that saved races; it w as his penance but here she stood before him, woman and time vortex. Rose Tyler was more than all of them and she wiped out the Daleks again, with the wave of her hand. She was neutral, influenced by what had been and what should be, and able to put it all back to rights.
He was never more glad for a human's company than when he chose to die for her.