The novel begins on the planet Veridian III and takes place shortly after the events seen in the motion picture Star Trek Generations.

Using alien technology, the Borg bring Kirk back to life and his katra is restored, but false memories are implanted to turn him against the Federation.

Simultaneously, Picard and Dr. Beverly Crusher are participating in a strike team in a Federation expedition to an assimilated colony, where they are forced to sneak on board the fleeing Borg vessel.

Kirk is eventually captured on Deep Space Nine attempting to kill Commander William Riker, and the implant that was responsible for his false memories is removed by the joint efforts of Dr. Julian Bashir and Admiral Leonard McCoy; McCoy acts as an advisor during the surgery while Bashir's younger, fitter hands perform the operation.

Although Kirk retains the drives implanted in him by the device, leading him to a confrontation with Picard in a holodeck re-creation of the original USS Enterprise, Spock is able to remove the commands thanks to a mind meld.

Taking a Defiant-class starship (renamed Enterprise for the mission), the Enterprise-D senior staff, accompanied by Kirk, Spock and McCoy, travel directly to the Borg homeworld thanks to a stolen transwarp drive.