A massive energy cloud has appeared in Klingon space and threatens the Federation. The USS Enterprise is undergoing a refit under her new Captain, Willard Decker (Stephen Collins), but James Kirk (William Shatner), now Chief of Starfleet Operations, takes her over and charges off to intercept the cloud. There are a series of problems with the untested refit, causing tension between Kirk and Decker but Spock’s (Leonard Nimoy) timely appearance helps defuse things. Enterprise catches up with the cloud and enters it, only to be trapped by a giant alien vessel that abducts navigator Lieutenant Ilia (Persis Khambatta), Decker’s past love, replacing her with a robotic probe that reveals that she/it has been sent to study the "carbon units" (humans) by something called V'ger. Spock mind melds with V’ger to discover that the vessel is V'ger itself, a living machine cobbled together by an alien race from the damaged remains of the unmanned scientific probe Voyager 6. The aliens misunderstand its programming as instructions from God, so V’ger wants to destroy humans as being imperfect. Decker and V’ger as the Ilia probe merge, granting V’ger compassion and thus saving Earth and the Federation.