The Emperor=The Face of Boe
All of Chaos=SILENCE WILL FALL voice thing/More Dreamlord?
Old Ones=Time Lords
Space Marines=Sontarans again (Clone race, dedicated to war?)
Tyranids=Some giant swarm meat-eating thing (Vashta Nerada?)
That's my two cents on how it'd be happening.
Bring on the Dreadnought Class Cybermen walker thing (It really is Dreadnought class. Read it in a book about the Doctor Who villains).
Doctor: Oh, the 41st Millennium, always hated this place. No one wears bow ties.
Ethereal: What is that human?
Doctor: Oh no, I'm a Time Lord. Are you a Tau? Shame, they got eaten by the Tyranids.
Ethereal: YOU WHAT?!
We need to figure out a scenario where the Doctor survives. Let's put him with some Eldar, he'd like Craftworld Eldar. I think.