Phoenix (Indefinable Magic).

Prose Doctor Who does Fantastic Beasts and Where To Find Them, pondering what might happen if that sort of book was granted sentience and went about trying to rewrite reality to reflect its contents. A perfect Short Trips concept, too small to sustain a novel but visually interesting enough that you would love to see it on screen.   The plotting is fairly simple, a bystander listening to the Doctor exposit on his foe before defeating it, but James Goss provides a few twists on the formula as he reveals the nature of the The Bestiary of Legendary and Magical Creatures and it's uncanny animals.   One of the features of Goss's writing is to misdirect his audience and take full advantage of the media within which he's working and arguably, despite what I said earlier, this story simply wouldn't work on audio or anything else.  Notably, for the purposes of this project, he has one of the adversaries seemingly allude obliquely to the Time War, as it was assumed to have happened when the book was published in 2009. 
Placement: Since it's ambiguous as to whether this is actually him, I've bunged it in "Almost, but not quite, entirely unlike the Eighth Doctor."