The Doctor has done many things over his long life that he’s not proud of, but one stands out above all, and the burden of shame and regret is heavy on his shoulders.
If allowed to continue, the Daleks would have destroyed every other race in existence; he couldn’t allow that. He thought of himself as a healer; someone who fixed things, made them better, someone who helped others. He wasn’t a killer, and yet…
To end the Time war, he committed genocide not once but twice, destroying his own people along with the Daleks.
And it didn’t even work.