As part of this plan, Admiral James T. Kirk assumes his former command of the ship, angering Commander Willard Decker, who had been overseeing the refit as its new captain. With many of the former crew members of the ship aboard, the Enterprise embarks on its journey, however, testing of its new systems goes poorly, resulting in further stress between Kirk and Decker. Many problems are resolved by the addition of Vulcan science officer, Commander Spock, who had been on his homeworld of Vulcan, undergoing the kolinahr ritual. His failure to complete kolinahr and purge his emotions has led him to seek his answers on the Enterprise, explaining, "On Vulcan I began sensing a consciousness. Thought patterns of exactingly perfect order. I believe they emanate from the intruder. I believe it may hold my answers."^[1]

The Enterprise intercepts the alien cloud, survives its initial assault, and journeys inside the cloud, finding a vast alien vessel, which draws the starship inside. An alien probe appears on the bridge and abducts navigator Lieutenant Ilia, who is replaced by a robotic probe that reveals that she/it has been sent to study the "carbon units" (humans) by something called V'ger. Decker is distraught over the loss of Ilia, with whom he had a romantic history, and is troubled to be assigned to get information from the mechnical doppelganger, which he discovers has Ilia's memories and feelings buried within. Meanwhile, Spock takes a spacewalk into the alien vessel, and attempts to telepathically mind meld with it. In doing so, he learns that the vessel is V'ger itself; a living machine. He also comes to terms with his emotions, realizing that the pure logic V'ger represents is "barren...cold."^[1]

The ship gradually journeys to the center of V'ger, where V'ger is revealed to be the unmanned scientific probe Voyager 6, which was part of the Voyager program, and (fictitiously) launched in the "twentieth century". The damaged probe was found by an alien race of living machines that interpreted its programming as instructions from God to "learn all that is learnable" and return that information to its creator. These machines made V'ger into something capable of fulfilling that mission, and "on its journey back it gathered so much knowledge that it achieved consciousness itself!" However, Spock realizes that what V'ger lacks is the ability to give itself a purpose other than its original mission. Having learned all that is learnable on its journey home, which took V'ger across the Universe, V'ger finds itself empty and without a purpose. Only through the creator can V’ger begin to explore illogical things, such as God, other dimensions, or higher planes of being. In the climax of the film, V'ger (in the person of the Ilia probe) merges with Commander Decker and then vanishes into a higher realm of being, and thus Earth is saved by the crew of the Enterprise.