The Confederacy — Humans, Ramanthians, Hudathans, Clones — have decided to band together, as the only way to fight a vastly superior threat called the Sheen (a robotic fleet led by an AI called the Hoon). The Sheen are after the Thrakis. There is a political plot by the Ramanthians and Thrakis, with the Clones embroiled into it.
The Confederacy manages to agree to rearm the Hudathans, to much misgivings by many members of the Confederacy and the Hudathans.
The coalition forces finally meet the Sheen, learn of a devastating secret weapon of the Thrakis, and also discover a secret link between the Thrakis and the Hoon (though this last part seemed abruptly and conveniently inserted into the plot).