We have a solid basis for believing that the Special will finally show the final moments of the Time War, in which the Doctor who uses a weapon referred to in 'End of Time' as 'The Moment' to destroy the Daleks at the cost of also killing the Time Lords, something he did because of their degeneration into insanity and the creation of superweapons such as the Nightmare Child (whatever that is). This isn't just wild speculation though, we do have some evidence to back this theory up.
- It's heavily implied, if not stated outright, that John Hurt's Doctor is a prior incarnation, not the next actual Doctor. The announcement of the actual 12th Doctor pretty much confirms this.
- Going back to Ecclestone's series, the Time War is mentioned constantly but never shown. A key episode would be Dalek, in which the Doctor actually tortures the dalek he finds in the vault, even orders it to kill itself and screams hysterically at it, tries to shoot it, etc. Add that to David Tennant's treatment of his double at the end of Journey's End, in which he references that when he first met Rose he was full of hate, born in battle, and we see that The Doctor was once vengeful and somewhat dark.
- When John Hurt says 'What I did was in the name of peace and sanity', we strongly believe he is referencing the use of The Moment (which the Time Lords state outright he has in his possession in the final days of the Time War, as seen in End of Time) to end the insanity again referenced in End of Time by David Tennant regarding the Time Lords creating terrible weapons and basically unleashing Hell.
- We know the Doctor feels shame over his actions at the end of the Time War, seen repeatedly through every season. In Dalek, he flat out says he is responsible for the ultimate destruction of the daleks and Time Lords, he says to the imprisoned dalek 'I made it happen'.
So from that all taken together, along with the setup being that the Doctor did something terrible that goes against everything the name of the Doctor stands for, on top of the fact that finally seeing the Time War in a cinematic release in 3D would be pretty beyond epic, it seems fairly obvious that's how the episode would, or at the very least SHOULD play out.