Tasha Lem warns the Doctor in ‘The Time Of The Doctor’ that should the Time Lords return then the Time War would be reignited. We have seen how the whole of reality was nearly destroyed during the last Time War.
This is a problem that will need to be resolved at some point if the Time Lords are to return in the future. There is no point in having saved them if they are forever trapped in a pocket dimension.
The universe once did exist with the Time Lords in it so how can it be restored to that point? The problem would appear to be the proliferation of time travel technology. It used to be that very few races possessed it and when they did it was very basic compared to the Time Lords.
Now it would appear that many have it, including humans, Daleks and possibly Cybermen. What is more they have used this technology to extensively interact with different periods in history. The Dalek kidnapped the Ponds in ‘Asylum of the Daleks’ and the Church were able to establish footholds in the dawn of Earth’s past, also kidnapping others. Not to mention all the races that formed an alliance to create the Pandorica in 102 AD.
The last Time War occurred between the Time Lords and the Daleks but if the conflict began anew there would be many more participants. Things would likely escalate much more quickly.
It is said that the Daleks initiated the Time War due to the discovery that the Time Lords had attempted to wipe them from existence in the events depicted in ‘Genesis of the Daleks’ but how soon would it be before they or another race begin a new Time War even without the presence of the Time Lords?
If the Doctor or your PCs are ever going to bring the Time Lords back a solution must be found. There are a variety of ways that this can be addressed.
Remove Time Travel Technology
The PCs must travel into the time stream of each of the races and prevent them establishing time travel technology. This can allow you to showcase each of the races approach to time travel and the steps they took along the way.
While they might want to kill the inventors of the technology ‘Doctor Who’ favours a less bloody solution. They could simply sabotage their attempts, persuading the race not pursue this development (and possibly convince them it is impossible).
They might also highlight the dangers of time travel to the race. If it is shown to be too dangerous the more agreeable aliens might halt their time travel experiments for fear that they’ll destroy themselves in a paradox.
Aliens might become aware of this and use their time travel technology to protect their history or eliminate the PCs before revisions to history catch up to them. This is a literal race against time.
Wait For War
Since the chief concern is the start of another Time War the PCs could wait until the next conflict begins. If they were willing to take the risk they could try to escalate events, pushing one side or the other to instigate the conflict.
Now the PCs just have to stay long enough to release the Time Lords in the chaos. This could make the situation worse or the Time Lords could have an advantage, given their experience with time travel technology that far exceeds their opponents.
Form An Alliance
If the PCs can persuade other time travel capable races to side with the Time Lords then they can find allies to help them. If enough join them then when the Time Lords are freed they will have such a strong alliance that their enemies won’t dare to attack.
What will they need to promise in order for other races to ally with them? The Time Lords could find that they now have to share power and technology. Would they refuse and risk another war or agree and potentially weaken their position in the galactic community?
Could the PCs persuade the other races to allow the Time Lords to return. This is different from an alliance, in that the races would not support Gallifrey, only tolerate its presence. What assurances would they need before a race agreed not to begin the fight again?
It is possible that the PCs could persuade others that the Time Lords are needed to prevent another Time War. Their return could act as a deterrent to other races. Any act of aggression would have to factor in the involvement of the Time Lords, which might be a fight on one to many sides.
Call Their Bluff
It could be that the other races aren’t capable of fighting a Time War. It almost wiped out the Dalek race last time, would any other races dare take the same risk? Even the Daleks, with their rebuilt empire, might not have the resources to fight a Time War, especially after their sacrifices on Trenzalore.
The PCs could set out to find out if the various time travel capable races are actually able to carry out their threat. This would require them to probe their military capabilities, take stock of their available resources (ships, planets, etc) and their mastery of the technology.
Reboot The Universe
When the cracks in time threatened everything the Doctor had to reboot all of reality, with Amy’s memory serving as template for how things were restored. We know that there were some changes due to this.
If the PCs felt they had no choice they could try something similar. Obviously this would endanger everything and they would be opposed. This is desperate act and could actually make them appear to be the villains of the story.
If it worked then they could bring into an existence a universe without the time travelling races, leaving the way clear for the Time Lords to be returned. Would they be hailed as heroes or condemned for their actions?