In 2286, Kirk and company wait in self-imposed exile on Vulcan, monitoring Spock's progress as he remembers his past. On Earth, the Federation Council is urged by the Klingon Ambassador to produce Kirk for trial for his actions against the Klingons on the Genesis Planet. Ambassador Sarek denies the request to permit Kirk's extradition from Vulcan and defends Kirk before the Council. The council agrees, yet demands Kirk return to Earth to face his violation of nine Starfleet regulations. Caught between two different sides, Kirk finally decides to take the Klingon Bird-of-Prey to Earth to face the Council's charges. Spock, still suffering slightly from his fal-tor-pan, decides he must accompany his captain.

The crew arrives to find Earth in turmoil, threatened by a deep space probe that has drained all power and is vaporizing the oceans, producing a worldwide cloud cover which begins to block the sun. Because of the enormous storms ravaging the entire planet, Starfleet warns all approaching spacecraft to keep their distance.