As the U.S.S. Enterprise returns to spacedock for repairs following the battle with Khan in 2285. Kirk continues to mourn Spock's death. McCoy suddenly enters the Vulcan's sealed quarters, babbling incoherently. Upon reaching Earth, McCoy is hospitalized. Scotty is reassigned to the U.S.S. Excelsior and the newly formed Genesis Planet is decreed off-limits by Starfleet Command. Kirk is then informed that the U.S.S. Enterprise is to be decommissioned.

In Kirk's quarters, Sarek, Spock's father, confronts the Admiral, saying that Spock's body should have been returned to Vulcan so that his katra could have been stored in an ancient Vulcan repository on Mount Seleya. Sarek tells Kirk that he must retrieve the coffin from the Genesis planet and, since Spock performed a last-minute Vulcan mind-meld with McCoy, thus transferring his "katra" or spirit, the doctor must also return to Vulcan.