So, if the "After Darkness" storyline picks up right after the movie, do they mean right after the crash in San Francisco or the "One Year Later" bit? If it's a year later, it seems odd that the Klingons would have only known about Kirk's presense on the homeworld so late, or that Kirk would wait that long to question April. However, if this storyline attempts to fill the gap of "what happened in that year's time that had passed?" why is the Enterprise fixed already?
Hard to tell from just 7 pages, but it's those kind of questions that bug me more than the continuity issues that the comics have had with the two films. I understand and appreciate the film's needs to not get bogged down in exposition and detail that long time Trek fans obsess over, but I figure the comics can sevre that purpose.
In any event, I (for no reason except to think a five year exploration mission wouldn't happen if the Klingon threat was as bad as April and Marcus would have us think) believed that by the time the five year mision started, the imminent threat of war with the Klingons subsided.
Of course, for all I know, the Organians could get involved with this storyline before it's over! That said, I like the idea of not knowing how much of this alternate timeline will conform with the general direction the prime one. Especially if Praxis already exploded, and the Klingons found a way to cope without resorting to putting out peace-feelers with the Federation.