The Enterprise tries to save an unidentified ship plunging into a supernova but is dragged into a universe where time runs backwards. Their only hope to return home is Commodore Robert April, the first commander of the Enterprise, who is onboard on a retirement trip.
Dr. McCoy is arrested and held responsible for causing a plague that ravaged the planet Dramia Two, where he performed a mass-inoculation 19 years earlier.
When Spock is stricken by a disease fatal to Vulcans, the Enterprise is to meet a freighter with a load of drugs that provides the only cure, but Orion pirates attack the ship and Kirk must track down the Orions and the drug before it is too late.
Kirk leads a party to retrieve a religious relic that was stolen. However, he is faced with sabotage from within the group by someone who doesn't want the relic to be found, which will trigger an intergalactic jihad.