Doctor Who: Unnatural History
Around the turn of the century, the Doctor underwent regeneration in San Francisco. A few years later, when he goes back, it appears that the catastrophic events that almost sent the entire Earth into cosmic oblivion have had an impact. San Francisco served as the anchor, and now there is a dimensional gap. There have been reports of gryphons, unicorns, and other strange and wondrous creatures, as well as more evil ones. Sam, the companion of the Doctor, is revealed and literally changes as a result. She has dark hair and has never met the Doctor before.