I am thinking he was the Doctor during the
start of the Last Great Time War. During the start of the war he was probably a soldier like everyone else. Consider the whole Doctor name is about helping not harming people his actions in the war probably didn't sit well with all the other incarnations. He probably committed horrible acts of violence and death repeatedly give the time nature of the war. Lost battles become victories then lost battles. Billions die, are brought back, die again, over and over. It probably created a kinda of limbo effect where the Doctor sees the fallen as never having true rest in death. There are a few lines such as this in the series hinting at how bad the war really was. John Hurts pays this Doctor. I think in his mind the Doctor(s) has isolated Hurts from his memories. A kind of motivated forgetting or psychogenic amnesia people have during horrible events in their lives; war, abuse as a child, etc.
I think the special will be able the Doctor(s) having to face these memories due to jumping into his own time-line. He will have to cope with these actions and also come to a realization that many of his other actions were not always helpful or "do no harm" real doctors follow. After all the races he fought against while helping others since other races are in the special as well.
I've always wondered if the Doctor is a paradox generating entity or a physical embodiment of a variation of the grandfather or temporal paradox itself. For example in one of the early Eccleston episodes he takes Rose, and some other male character I've forgotten, to the 4th Great and Bountiful Human Empire. He says things are not right for what he sees as correct history. He "corrects" whatever errors in the timeline. Perhaps what he sees as "correct" history, his past, is only true due to his actions in the present. The past is only true due to what he does in the present and future. The normal time-line and the Doctor's time-line are disconnected. The normal universe time is A-theory, point A to B to C. The Doctor's is only A-theory to him but has the effect of B-theory time, point A to B to Z to A, etc. So in this way Time-Lords are not masters of Time, players, but merely pawns on the chess board like everyone else.
Topic: The Doctor Who Appreciation Society