It has been revealed that the Doctor during the Time War committed genocide of the Time Lords during fighting with the Time Lords against the Daleks. But what if the Doctor that did those things in the war was a future version? What if the Doctor fought for both sides of the Time War to orchestrate an escape, the past version fighting for the Time Lords and the future version fighting for the Daleks, perhaps causing both sides to fight? The past version, knowing it was the only way he could escape, accepted the future version’s help, but in doing so, accepted his own future and knows he must come to it at some point.
The Doctor has mentioned the Time War at many times over the series with references becoming more specific over time, which could represent him becoming more and more the Future Doctor. This especially comes up in Series 6 (Fear me, I’ve killed all of them), where he avoids the Silence using River to kill him. Many times throughout the series, the Doctor has attempted to sacrifice himself or act more frivolous about it, but the companions have been used by the Doctor to give him the purpose of protecting them instead of just killing himself to stop everything. But in the act of avoiding his death on Lake Silencio, he didn’t need to protect his companions (since they were just on a beach), which was the Silence’s calculated attempt to bring down the Doctor in a way he would like, but he still avoids it. This could represent him fully recognizing his future and wanting to become it.
This theory would explain why the Daleks know of and are so afraid of the Doctor, since he fought their race and fought with it, becoming a traitor to them. It would also explain why Clara wipes the memory of the Doctor from the Dalek’s memory: to set the stage for working for both sides. Also I think the Doctor has been a Dalek since the Christmas episode, and Clara and everything else he’s experienced is in the Dalek’s head, which would set the stage for him participating back in the Time War for the 50th.
Some of this might be right, anyway. /Mopsical