The bit that always confused me (okay, one of the bits that always confused me) was this excerpt from the manual text:
You've been one busy security officer.
You repulsed the Pfhor attack on the colony ship Marathon, uncovered and reawakened the fabled 11th clan of the S'pht and their ancient AI Thoth, rescued the stranded human survivors of Tau Ceti and halted the Pfhor advance on Earth...
And you delivered yourself from your "service" to Durandal, the rampant A.I. whose taste for irony is second only to his unpredictability. Durandal, who at last sighting left to tool around the galaxy in a newly rechristened Pfhor vessel with a crew of S'pht comrades.
When did that last paragraph happen? It seems to me that the only way that could be true would be if the player's character were responsible for what's happening in Infinity, rather than being helplessly pushed around by Thoth, the Jjaro, or merged Durandal/Thoth from the future.