In ‘The Name Of The Doctor’ the Doctor and Clara journey to the final resting place of the Time Lord and his TARDIS, Trenzalore. In ‘The Time Of The Doctor’ they find themselves in that planet’s past and the Doctor is convinced that it is his fate to die there.
Thanks to Clara’s pleas the Time Lords help change that future, giving the Doctor a new lease of life. What does this mean for the events of ‘The Name Of The Doctor’?
The simplest answer is that at some point the Doctor still dies on Trenzalore. That it is still the scene of his biggest battle. This is certainly possible and would mean that all the events of ‘The Name Of The Doctor’ occur exactly as we saw.
The more complicated answer is that the timeline the Doctor and Clara visited showed what would have happened if the Doctor hadn’t been given a new set of regenerations and had indeed died of old age.
Since the Time Lords haven’t returned and a new Time War wasn’t initiated then we can presume that in this version of events the Doctor didn’t summon them through the crack. This does raise the question of why he didn’t do this with his last breath, especially as the inhabitants of Christmas were almost certainly going to die shortly after he did. Did he believe that leaving his people trapped was better than putting the whole universe at risk?
There are gravestones of soldiers, which you would assumed were placed by the Church of the Mainframe after the Daleks departed. Even with advanced technology this could have taken quite some time, since the battle extended for hundreds of years (and how do you mark the grave of a Silence?)
The problem with this is that we saw that the occupants of the Church ship had already been converted into nano-zombies. It is possible that another chapter arrived later to place the gravestones or that the Daleks let their slaves return to their default behaviour and carry out this task (maybe while they waited to be reassigned to other parts of the universe).
Who was it that arranged for the grave of River Song (who we know couldn’t possibly have taken part as she was already dead by this point) to lead to a secret entrance into the TARDIS?
Since the Doctor thought that the future he saw was coming true he probably left instructions with Tasha Lem. The secret entrance could be the same way that she is able to enter the TARDIS later to bring Clara.
Was the Doctor tempted to leave a means of salvation for himself, since he knew his younger self would eventually arrive on the planet? He could have placed a coded message on a grave stone, buried something that would help near the landing site of the previous TARDIS or placed something within his own TARDIS to be found as his younger self approached his tomb.
He might not, fearing that any disruption to the time line might prevent Clara from saving him from the Great Intelligence. If he did then now that future has been averted he might have to recover those warnings or ways to change his present.
How would time reshape itself if Trenzalore is no longer the place where he dies? Possibly the same events could occur on whatever does now become his final resting place. They’d still be a scar in time that the Great Intelligence could try to use against him. The names might change but the details would remain the same.
If his final resting place isn’t known then not only does the Great Intelligence not have a means to change the Doctor’s history but Clara won’t splinter herself into multiple incarnations to meet the Doctor in different time periods.
This would significantly alter ‘Asylum of the Daleks.’ Would the starship ‘Alaska’ have still crashed into the asylum without Oswin Oswald onboard? Could the Doctor, Amy and Rory have safely navigated through the asylum without the guidance of Oswin? Would they have escaped the Parliament of Daleks if she hadn’t wiped their memories?
Similarly ‘The Snowmen’ would have been changed without that version of Clara. It is possible that the Doctor might have been become aware of the Great Intelligence and the animated snowmen as the situation worsened. Would he still have been able to defeat the entity without the Latimer family sorrow at Clara’s death neutralising it?
‘The Bells of Saint John’ is unaltered by the loss of the events of Trenzalore, aside from the Doctor trying to work out why he keeps meeting Clara. We are yet to discover who the women was that gave Clara the Doctor’s number but this could still occur, initiating the first contact between them. Regardless the fact that someone is calling him would bring the Doctor running.
The Great Intelligence’s involvement in that plot can occur completely separate to his eventual plan. All this would mean is that he’d have to find another way to get revenge on the Doctor at a later date.
All of these revisions could have already taken place. The Doctor and Clara might remember different version of events or find that their memories don’t match those around them.
We’ve seen that the universe is more resilient to changes in time that we first thought. In your own campaign you can run multiple versions of these continuity. If the PCs aren’t connected to the Doctor they might not even realise the significance of these continuity errors.
If you want to run an adventure featuring the 11th Doctor you could base adventures around this premise, seeing if the PCs can survive without the involvement of Clara. Will things turn out for better or worse.
You could also set games in a future where the events of Trenzalore did or didn’t happen, based on your preference. As above you could also do both, allowing time to adjust itself following the events of ‘The Time Of The Doctor’.