I haven't run DWAiTAS since the start of the year but in recently getting the desire again to do so I need to work out a problem that came up the last time.
It was a homebrew scenario involving an experimental prison colony on another world, monsters of the imagination made manifest and a (hopefully) recurring minor villain. However, after a certain point the players decided that they couldn't defeat the villain so just legged it with the surviving staff of the prison into the TARDIS and took then back to Earth before vanishing off into time and space. Fair play but it really (for me) ruined the scenario with an anti-climactic ending and ditched my enthusiasm for the game at the time.
Other than being a dodgy GM and railroding that element how would the rest of you keep the characters in the story if it happened in your games?
"There are worlds out there where the sky is burning, and the sea's asleep, and the rivers dream; people made of smoke and cities made of song. Somewhere there's danger, somewhere there's injustice, somewhere else the tea's getting cold. Come on, Ace. We've got work to do."
The first rule of story for a gamemaster is to remember that it's a combined effort between the players and him/herself. Any "story" which involves the GM pushing the players from predetermined plot point to predetermined plot point is essentially railroading - so adapt to their unexpected choice of direction.
I'd look into two things - first, ask they players what they thought of the hopefully recurring villain. It could be they believed the villain too powerful to defeat - in which case that may be something to take and run with. This "minor" villain just might be your Master or Davros - coming back with a vengeance time and again.
On the other hand, if the players weren't feeling engaged by the villain and preferred to just hoof it out of boredom, the best thing to do is let the story move in another direction, one which the players are more inclined to enjoy while still finding suitably challenging.
My suggestion for picking up the game is to ask at least one of the players "So, where is the TARDIS going this time?" and put together a storyline based on a destination place and time of their choosing.
Establish that fleeing in the TARDIS is not a viable consistent option from the outset. State it out of character, mentioning that there may be times it's reasonable but that it generally isn't The Way Things are Done. And add that there are times when it won't be an option in-character, which will be set up beforehand.
(This is where the series occasionally had the TARDIS fall off cliffs, get stolen by Daleks, break down and need a vital part, be on the other side of a section of the station with a hull breach in the way and so on.)
It might also be a problem with how the players perceive the game. After all, the average Doctor Who group isn't much use in a stand-up fight, and Running does come before Fighting on the initiative track, so they might think it's their best option more often than it really is. Reminders of other things they can do, and setting pointers to environmental tricks they can use, could help. So establish that the colony's defences do X and could be jiggery-pokery-ed to do Y as well early on, about when you have the TARDIS drop into an inconvenient mineshaft.