The reason this book is out of print (and so few fans have read it) is because it was yanked off the market for being "in bad taste" around the time that Roddenberry began cracking down on Trek novels that he personally didn't like. (In the mid-1980s. See chapter 17 of his biography, "Star Trek Creator," for more on that aspect of Trek history.) At any rate, the very idea of a censored Star Trek novel was so intriguing to me, I just had to track down a copy and read it!
The plot opens with a number of Enterprise crewpersons having some very disturbing dreams. In the case of Kirk and Spock, they both have the same dream, in which Spock is captain of a starship that's not the Enterprise, and Kirk is a young ensign aboard that same ship. As it turns out, the dreams are really bleed-throughs from another universe that was created by Romulan time-tampering. The Romulans, in an attempt to go back and change history in a way that would eliminate the Federation, have created Second History -- and it's not stable. On a deep subconscious level, many people in Second History are still linked to First History (the original timeline) and, in cases where their roles are not the same in both worlds, the disparity is causing insanity. And its spreading. If the original timeline is not restored soon, the whole universe is in danger of going mad.
What might be offensive to some people is that Ensign Kirk of Second History is a pretty messed-up character. He's a bitter young man who gets into fights with other crewmembers, has spent some time in prison (although, it is pointed out, the evidence used to convict him was was circumstantial and he maintains his innocence), and was drafted into the Fleet against his will. (The draft is one of the differences that Second History introduces.) He's also misusing a dream suppressant drug to try and stop the nightmares. This is certainly not the way we want to see Our Hero portrayed -- but then again, it fits the plot. I mean, if the Romulans really want to put the Federation out of commission, wouldn't it make sense to get the highly-competent James T. Kirk out of the picture? Besides, we've seen Kirk acting "weird" before under various alien influences, so why would this scenario be any worse? There's also an element of "there but for the grace of God go I" in this story, making us realize that, given the wrong circumstances, anybody's life can take a bad turn. And it can also be righted again.
Eventually, the Second History versions of Kirk and Spock figure out what's happened. (A nice touch is that this is accomplished by a mindmeld that taps into the deep friendship between them in First History, which still links them on the subconscious level.) Ensign Kirk quits the drug cold turkey, gets his life together, and helps Spock try to figure out a way to save the universe. To tell you any more would be a spoiler, except to say that this book is well worth reading --- that is, if you can find a copy.