The U.S.S. Enterprise is appointed to transport ambassadors from many worlds to the Babel Conferences. Among those aboard are Ambassador Sarek of Vulcan and his human wife, Amanda — Spock's parents.
Keeping peace aboard his ship is complicated for Kirk by an unidentified vessel following the U.S.S. Enterprise and high tensions running among delegates on board. At a cocktail party, Ambassador Gav, a Tellarite, quarrels openly with Sarek about the admission of Coridan into the Federation. When Gav is later murdered, circumstantial evidence points to Sarek. The strain of such an accusation causes Sarek's already existing heart condition to worsen and he has the Vulcan equivalent of a heart attack. McCoy battles with less familiar Vulcan physiology to try and correct the damage. Spock is needed as a blood donor for the operation.
When Kirk is attacked by Thelev, an Andorian, Spock assumes command of the Enterprise, and refuses to participate in McCoy's operation on his father. The Vulcan insists that they identify and stop the vessel that is following them. Kirk fakes recovery and returns to the bridge, freeing Spock to go to the sickbay and assist in his father's surgery. On the bridge, Kirk must deal with the unknown ship, now in contact with someone on board the U.S.S. Enterprise. A search uncovers the fact that Thelev is not Andorian, but a surgically altered Orion, put on board to disrupt the Babel Conference.
The unknown ship attacks the U.S.S. Enterprise and is defeated. Rather than be captured, it destroys itself and Thelev commits suicide. With Spock available for the blood transfusion, Sarek's operation is a success and he recovers. Father and son make peace, realizing they have a common bond that transcends their differences. Kirk returns to sickbay for treatment of the knife wound caused by Thelev and McCoy gets the last word.