• James T. Kirk: William Shatner
• Spock: Leonard Nimoy
• Leonard "Bones" McCoy: Deforest Kelley
• Chekov: Walter Koenig
• Sulu: George Takei
• Uhura: Nichelle Nichols
• Valeris: Kim Cattrall
• Sarek: Mark Lenard
• Gorkon: David Warner
• General Chang: Christopher Plummer
• Federation President: Kurtwood Smith
• Klingon Ambassador: John Schuck
• Admiral Cartwright: Brock Peters
• Azetbur: Rosana DeSoto
• Martia: Iman

A colossal explosion on the Klingon moon Praxis sends intense shock waves through space, which are encountered by the USS Excelsior in its third year of duty under Captain Sulu. The Excelsior is damaged by the leading edge of the energy burst, but regains her balance. When offered assistance, the Klingons tell Sulu to mind his own business and stay out of their territory.

Later, on Earth, the command crew of the Enterprise is invited to a top priority, high-security briefing at Starfleet Headquarters, where it is revealed that one of the Klingons's' main sources of power, located on Praxis, released radiation that will eat away the Klingon home world's ozone layer in roughly fifty years, and the Klingons, whose economy is devoted entirely to military development, are unable to combat the deterioration of their planet without aid. Spock, acting as an ambassador, has opened the door for discussions with Chancellor Gorkon of the Klingon High Council, and has taken the liberty of volunteering Kirk and the crew of the Enterprise - both of which are three months away from mandatory retirement as Starfleet prepares to decommission the ship itself - for the duty of escorting Gorkon and his party to the first Federation-Klingon peace talks.

Over dinner on the Enterprise, the Klingons and the Starfleet officers seem to be unable to avoid eventually insulting or offending each other, and General Chang seems more interested in Kirk's reputation as a warrior than in peace. The Klingons return to their ship, and shortly afterward, torpedoes from the Enterprise's direction pummel Gorkon's ship, and two figures in Federation space suits beam aboard and kill the Chancellor and many of the Klingon crew. Still unsure of what has happened - Scotty finds that none of the Enterprise's torpedoes have been fired - Kirk surrenders when Chang threatens to fire on the Enterprise point-blank. Kirk and McCoy beam over, where McCoy tries to save the dying Gorkon, but with Federation medicine's limited knowledge of Klingon anatomy, McCoy cannot prevent Gorkon's death. Kirk and McCoy are arrested and given a trial where Chang's unusual evidence - including entries from Kirk's personal log stating his distrust of Klingons since they killed his son - insinuates that Kirk was behind the assassination. Kirk and McCoy are sentenced to work for the rest of their lives in the dilithium mines on Rura Penthe.

At Spock's command, the Enterprise conveniently develops a malfunction that prevents them from receiving Starfleet's order to return home while the crew searches for the equipment used by the two Starfleet officers who assassinated Gorkon. A few leads appear, but then are revealed to be false alarms - someone is deliberately trying to lead the investigation off track. In the meantime, Kirk and McCoy fight for their lives on Rura Penthe but are helped by exotic fellow prisoner Martia, who warns Kirk that even in the penal colony, there is a price on his head. Martia helps them escape, hoping that Kirk, who she says is the most attractive prisoner to appear in a long time, will repay her somehow. During their escape, Martia is revealed to be a shapeshifter, and perhaps not even a true female. Kirk realizes that the escape has been too easy and that Martia is the one out for he and McCoy. Martia changes into a copy of Kirk, but when the prison guards catch up, Kirk tricks them into shooting Martia instead. Bluffing their way past Klingon border guards, the Enterprise crew beams Kirk and McCoy up just before the two would have been executed.

After returning to the Enterprise, Kirk and the others discover two dead crewmen - the assassins - and realize that there is one more conspirator. Kirk suggests laying a trap by announcing to the crew that the dead crewmen are alive and in sick bay awaiting the court reporter, which would lure the culprit to sick bay to kill the two crewmen before they could talk. The ploy works, and the conspirator is Lt. Valeris, Spock's trusted protégé'. Spock forces a mind-meld with Valeris to find out who the main conspirators are, and discovers that Klingons and a member of the Federation top brass are already cooperating peacefully - to ensure that peace is destroyed by the assassination of the President of the Federation. Kirk contacts Captain Sulu, and their two ships head for Khitomer to save the President and reveal the conspirators, but time - and Chang's prototype Bird of Prey that can fire while cloaked (the real source of the attack on Gorkon's ship) - are against their efforts to save the negotiations.