As far as I can remember, the plot summary was something like this: "Due to <some sort of negative space wedgie>, the Daleks have been able to invade the Star Trek universe. They have teamed up with the Klingons, and are in the process of destroying everything in their path. In order to stop them, the Doctor and the crew of the Enterprise have teamed up."
I am quite sure that it isn't the comic book. Assimilation2 is very good (I've read it), but I specifically remember that the story I am trying to identify is a book.
If it helps, I think it is set during the ToS era of Star Trek, although I'm unsure about when it was written.