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.

In a tragic accident, two crew members are killed in a transporter malfunction — one of which was the new Vulcan science officer, Sonak.

The accident behind them, Kirk gathers much of the crew together to deliver a mission briefing, stressing the enormous power of the entity they are faced with. After a relatively uneventful departure from Earth's drydock facilities, the U.S.S. Enterprise is suddenly faced with a giant wormhole and Kirk, unfamiliar with the design of the new vessel, almost allows the wormhole to destroy the ship. The U.S.S. Enterprise escapes, however, and is hailed by a courier vessel bearing Kirk's new science officer. Overcome with joy at seeing Spock, Kirk is soon confronted with a cold, withdrawn stranger.....