In 2271 an unknown, cloud-like entity descends upon several Klingon vessels and destroys them. Having monitored the surprise attack, Federation space station Epsilon IX is still unable to prevent itself from becoming the next victim of this vast, mysterious energy cloud.
Meanwhile, on Vulcan, Spock is preparing to undergo the rite of Kolinahr — the achievement of total Vulcan logic — and the purging of all remaining emotion. Just then Spock’s human half stirs in response to the cloud entity, interrupting his meditation and forcing the Vulcan masters to withdraw Spock’s admission to their ranks.
On Earth, the U.S.S. Enterprise is readying to investigate the cloud entity. Admiral Nogura is persuaded by Admiral James T. Kirk to hand over command of the newly refit Starship Enterprise to him, superseding the vessel’s present captain, Will Decker, who is unhappy with this new situation. Arriving on board the Enterprise, Kirk requests that Dr. Leonard McCoy, retired now, be recalled into service as the starship’s doctor. An unchanged, blustery Dr. McCoy comes aboard and replaces Dr. Christine Chapel, who steps down out of respect. Also on board is a Deltan navigator, Ilia, who in the past was romantically involved with Will Decker.