Unnatural History — Kate Orman

The Doctor regenerated in San Francisco at the turn of the millennium. When he returns there a few years later, it seems the catastrophic events that nearly sent the whole of Earth into cosmic oblivion have taken their toll. San Francisco was the anchor point, and a breach between dimensions has sprung up. All sorts of weird and wonderful creatures have turned up -- griffins, unicorns -- and things more sinister.

The Doctor's companion Sam is exposed and becomes a changed person -- literally. Her hair is dark, she has never met the Doctor in her life. With Fitz, he is able to convince her to help them put things right -- to sacrifice herself so that the old Sam may return. For stalking the turbulent streets is the sinister Unnaturalist -- a collector of genetic curios whose private collection will be much enriched by the Time Travelers.