In My Opinion! No, the plot isn't that complicated - the motivations and backgrounds of the actors are.
The plots:
M1 - You must survive the Pfhor invasion in the Tau Ceti system.
M2 - You do the bidding of an unpredictable AI to solve the mystery of a missing S'pht clan.
M3 - You are forced to traverse several timelines by an ancient S'pht AI to prevent the release of a malevolent cosmic force by a Pfhor superweapon.
The actors:
You
Leela AI
Durandal AI (and, later, liberated S'pht)
Tycho AI
The Pfhor & Client Races
The S'pht Missing Clan
Blake & Co.
Thoth AI
The background:
See Story, Marathon, Site, Web
Good luck on your book. Write EVERY DAY - even if it's only a page. Find an editor that has NO interest in whatever genre you are writing about. Don't take criticism personally.