When watching the recent Doctor Who story "Amys Choice" one of the things that disappointed me was the ending (if you haven't seen it, watch it - you will see what I mean) it was "finalized" as a story in a very short space of time with an almost disappointing explanation from the Doctor (and no I'm not giving away any more details than that).
ANYWAY back to point, such devices - whether it be plopping your players down in a “Land of Fiction" such as happened in the 2nd Doctor Story "The Mind Robber", or trapped in a "Realm of deadly parlour games" as the 1st Doctor was in "The Celestial Toymaker", or even trapped in a Virtual World like Donna was in the 10th Doctor Stories "Silence In The Library" & "Forest Of The Dead" - can be a VERY powerful tool in the hands of any Doctor Who Games Master.
Let’s face it, even though you have the whole of Time and Space to play around in - your hands as GM are fairly tightly bound.
Any "changes" made to the time-line have to be written in so they at least LOOK like they are changes (that actually aren't) or are "future" changes - so they don't affect the Whoniverse to dramatically.
Your last option as GM is the "rubber band" effect - change what you want, but and the end of the day the "rubber band" will only stretch so far and your story has to end in such a way it bounces back so everything’s normal - we've seen this in the series over and over again, the most recent (and dramatic) example being "The End of Time".
Using the "Fantasy" universes is really freeing for any GM - you can LITERALLY do what you want as a story, throwing all caution to the wind without worry of consequences to the time-line or being worried for the future of your games.
Its even possible to have that dreaded occurrence a "Character Death" and (if at all possible) get the player who's character is going to die "in on it" - that way you can milk it for all its worth, and possibly even illicit strong emotional responses out of your players when their friend and comrade lays down his life for his fellow travellers.
Beware though, you can't do these "fantasy" stories often - once per campaign AT MOST is my advice. If they become the norm, players start taking risks, and become very blasé about the whole thing - plus it can end up as very "dull" too.
Try a Walk on the Wild Side occasionally, your players will love you for it!