Following the catastrophic events on the Genesis planet, the USS Enterprise returns to Earth, heavily damaged. Admiral James T. Kirk is still reeling from the loss of his friend Spock, whose casket was launched onto the newly-formed planet. However, strange occurrences involving Dr. Leonard "Bones" McCoy indicate a connection to Spock. McCoy, acting erratically, is discovered to be carrying Spock's katra, his living spirit, within him. Sarek, Spock's father, informs Kirk that they must retrieve Spock's body to lay his katra to rest on their home planet Vulcan, or McCoy's life could be in danger. To honor their fallen comrade and save their friend, Kirk and his loyal crew decide to embark on an unsanctioned mission to recover Spock's body.

Defying Starfleet's direct orders, Kirk and his crew commandeer the now decommissioned Enterprise. As they set course for the unstable Genesis planet, they are unaware of the grave dangers that lie ahead. The planet, a scientific marvel turned deadly, is rapidly deteriorating, making the mission even more perilous. Moreover, they are not the only ones interested in Genesis. A group of Klingons, led by the cunning Commander Kruge, seeks the secrets of the Genesis device for their own purposes, leading to an inevitable confrontation between the two parties. With time running out and enemies closing in, the Enterprise crew must overcome both external threats and personal turmoil in their relentless search to find Spock.