The story begins several months after the conclusion of the previous comic, with the Decepticons in exile, and the Autobots freed of their merciless hounding.
Delayed, but not defeated, Megatron next turns his attention to destroying Bludgeon, the present day commander of the G1 Decepticons, and to reclaim leadership.
Prime discovers that the Elders reactivated it during the Autobots' absence on Earth, and that since the progress was never intended to be restarted, the Cybertronians were flawed immeasurably.
During the conflict, Starscream briefly gains control of the Matrix, but eventually returns it to Prime when its inherent goodness corrupts his program, Jhiaxus succumbs to an insanity long repressed that reflected his barbaric side and he nearly destroys Optimus before being consumed by the invading Swarm.
The name of the character Jhiaxus is pronounced "gee, axe us", this was an intentional joke by Simon Furman anticipating the short lifespan of the comic, which proved true.