The Editor suggests that he would change history so that the human race never exists. This does seem to be contrary his previous motivation. Mere moments before he’d indicated that he works for a consortium of banks. The enslavement of mankind is a long-term investment.
If we take it that these banks are alien (or indeed run by the Daleks) they gain nothing from wiping out humanity. Since they are motivated by the financial benefit of turning a population into consumer cattle the last thing they’d want is to eliminate this cash flow.
Given that we later learn the Daleks are using humans for genetic material to rebuild their empire they’d also not want to see them removed from history. There could be an even greater impact on their own history if none of the Doctor’s companions existed (unless that is all time locked).
It could be that this is a very elaborate suicide by the Editor. He is, after all human and it is possible that he couldn’t see any way out of his own enslavement. In all likelihood he’d have to go in the TARDIS without the Jagrafess due to its size and dependence on a coolant system. His plan to wipe himself and the rest of humanity for existence could then just be his idea.
Of course it could all be a bluff. The Editor is just taunting the Doctor, while he has him at his mercy. He might be trying to manipulate him into revealing more about time travel or forcing him to go along with him.
Regardless, the sheer damage that a villain could do with a time machine is terrifying. It is a situation that happens very rarely in Doctor Who, with the Master stealing the TARDIS in ‘Utopia’ and Mel hijacking the time machine at gun point in ‘Let’s Kill Hitler’ being most notable recent examples.
This is probably wise as the majority of the time the Doctor and his companions should make things better with their arrival, not worse by letting their time machine fall into the wrong hands.
If this happens too frequently in your campaign PCs might become very paranoid about where they leave their own TARDIS. They might hide it, land it in inaccessible places or take turns guarding it.
They will keep its existence a secret, fearing what people will do if they know about it. No NPC will be trusted and they might take great steps to avoid being followed back to the TARDIS. This would make taking on new companions even more difficult.
This is a shame since the TARDIS is a magical presence in Doctor Who. The Doctor often freely reveals it to friendly people he meet, such as inviting Sir Robert and a police sergeant inside in ‘Full Circle’. Players should have enough trust in the GM that they can let the right people inside.
Used sparingly this can be the start of a good adventure. Ideally the PCs will want to stop the enemy from getting to their TARDIS before they do. This could lead to a chase or a quest as both sides race against each other or try to get vital quest items (like the key).
This can take an added twist if the TARDIS has fallen down a chasm, into the ocean or is floating in space (as it occasionally does). In this situation both sides will have to work out how they are going recover it.
If the villain does get the TARDIS are the PCs with him when he uses it? They could be there under duress, as in ‘Let’s Kill Hitler’ or just held captive within the recesses of the TARDIS while the villain rewrites history. If he has the only key he could lock them inside so even if they get free they won’t be able to get out. He might take a vital component from the console to prevent them from taking off without him.
The PCs could also be left stranded, as in ‘Utopia’. Their first task will be obtain some way to pursue their quarry whether it be using a vortex manipulator or another TARDIS. This could take them directly to the stolen TARDIS or force them to pursue their enemy across the eons, fixing the damage he causes in his wake.
All is not lost if a villain does obtain a TARDIS. Most obviously, although possibly too anti-climatic, they might not actually be able to use the TARDIS at all. Some companions have managed to activate some basic functions of the time machine only River Song has shown skill that acceded the Doctor’s (with the exception of Romana) and she had the advantage of being taught by the TARDIS herself.
If the villain has the knowledge to work it (possibly stolen from the memories of a Time Lord PC) then things become much worse. The PCs must hope that either the villain can’t navigate to a place in history where they could cause problems (maybe they only go to alien worlds) or the TARDIS resists them.
Time travel is difficult and villains could find that it is more resistant they anticipated. Despite their best efforts they might be unable to change what they want or their actions have unexpected consequences that cause the villain more problems.
The Doctor Who unbound audio ‘He Jests At Scars’ demonstrates what can happen when a villain starts to alter their own timeline, threatening their very existence.
These problems can slow a villain just long enough for the PCs to catch up or be able to fix what ever damage they have already caused. They can then reclaim their TARDIS and think of ways to punish the villain.
Sabbath from the 8th Doctor BBC books is an example of an ongoing time travelling villain that can be a worthy foe for any Time Lord. Not only did his meddling in time cause problems for the Doctor to solve but he was liable to arrive in the middle of an adventure and make things more complicated by solving them using his own methods.