Admiral James T. Kirk (William Shatner)is called upon to collect his old crewmates in order to save humanity from a giant, hostile alien vessel steadily approaching Earth and destroying everything in its path. The complex alien life-forms apparently possess such an advanced intelligence that even the brilliant Mr. Spock (Leonard Nimoy) fails to comprehend the massive structure that contains them. There is tension on the ship, as well as in the universe, as Commander Willard Decker (Stephen Collins), the Enterprise's new captain, is relegated to being Kirk's assistant. In addition, Dr. Leonard "Bones" McCoy (DeForest Kelley), the lovable, crotchety doctor who is constantly at odds with Spock, must be tricked away from his life of relaxation to serve on a voyage he wants no part of. It's not long before the Enterprise is taken over by the alien entity, and navigator Ilia (Persis Khambatta) is abducted. When she is returned to the Enterprise, she informs Kirk that unless the entity is united with its creator, it will destroy the Earth.