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.

However, Starfleet refuses to allow the antiquated U.S.S. Enterprise to leave spacedock. Released from the hospital and faced with this news, McCoy tries to hire a craft to go back to the Genesis planet. He then starts a brawl and is subsequently arrested, pending further psychiatric examination. The arrest proves futile, though, when McCoy escapes with the help of Kirk, Scott, Sulu, Uhura and Chekov. The crew then beams aboard the deserted U.S.S. Enterprise. To avoid pursuit, Scotty removes an integral engine part from the U.S.S. Excelsior and, knowing that they've all probably destroyed their careers, the six friends take the Enterprise out for one final voyage.

Meanwhile, the Klingons have learned of the new Genesis Device and planet, and fear that it could be a new Federation weapon. Lead by the treacherous Captain Kruge, the Klingons set out to either destroy or capture the valuable device.....