You might think that a show about a time traveller would have a fair number of episodes about time travel, but this isn't really the case. Normally, the TARDIS is a magic door to a new adventure, and once you're there, you're there. Episodes where time travel is a major feature after the initial setup are much less common, although Steven Moffat is doing his best to change this...
The series has built up some (rather inconsistent) rules about time travel, from ontological paradoxes and how they apparently work even though they don't to the Blinovitch Limitation Effect saying that you can't meet yourself or you shouldn't meet yourself or you mustn't come into contact with yourself or that's okay as long as you're from a parallel universe or nothing else has happened or...
Generally, going back in time and having another go at fixing things is not on. Unless time itself has gone very wrong, in which case it is. I think. Anyway, there's a lot about this in a future supplement, but I'm not here to talk about how it works as that changes from story to story, I'm here to talk about the story in time travel itself.
11: Wibbly-wobbly, timey-wimey!
Time travel in the Whoniverse is a bit risky with an expert, and downright deadly without one. Step across a rift, try on a Vortex Manipulator or turn your back on the wrong piece of monumental statuary and you could find yourself lost in another time with no way back, assuming you're lucky enough to materialise somewhere capable of supporting humanoid life.
In keeping with the show's horror DNA, you could become the foundation of a ghost story as you disappear without trace, or try to contact your own time. Your best hope then is that a time traveller comes along and sees the problem and tries to rescue you.
So a lot of time travel stories are mysteries - what is this doing in that time, who is sending that message and from when?
One important question is how much control the PCs have over their travels. A fully capable Time Lord in a top-of-the-line TARDIS could stop an intergalactic war by altering the opposing factions' histories so that they never meet, but five people hanging on to the same reverse-engineered Weeping Angel heart will be lucky to land on solid ground.
The PCs will probably be somewhere in between, able to pull off some temporal stunts in an emergency but having to burn Story Points to do anything non-essential. An unreliable time travel method like the Doctor's TARDIS can be used to discourage too much going-back-and-checking, because it has a tendency to drop people in the wrong century or galaxy.
This raises another kind of time travel story, often a Big Emotional Episode - a character's personal history. Rose saving her father nearly destroyed the human race. Something to think about when you go back to see something...
Example: The Man At The Edge Of Time
Wherever they go in modern-ish Earth, the Doctor notices a man in the crowd observing them, looking at Emily and particularly Richard curiously. Always there, always too far away to get to. Who is he? What is he doing? What is he waiting to see...?