A difference that makes no difference is no difference. This is the main current in this book, when an overly powerful entity decides to put the most celebrated friendship in the galaxy to the test.
Not to spoil anything, but a phoenix rises from its own ashes to fly once more.
From the log of Chief medical officer Leonard McCoy: for the record, the primary cause of death was asphyxiation, though there were severe internal injuries as well. Fortunately, the deceased was knocked unconscious almost immediately and thus spared a great deal of pain.
"I've just spent the last 45 minutes comparing blood samples, dental records, even gene structure---and come up empty on all counts. There's no doubt as to the deceased's identity; no possibility this is an android, shape-changer, or what-have-you. The BODY IS that of the former commander of the Enterprise: CAPTAIN JAMES KIRK.