While exploring a "hypergiant" that will explode, the starship Enterprise makes peaceful first contact with an alien race known as the Vissians, and the two starships' crews begin to intermingle. Commander Tucker, becomes intrigued when he meets a Vissian couple in the Enterprisemess hall accompanied by another of their race who seems different and is referred to as "it". Tucker learns that the being, which has no name, is a "cogenitor" - a third gender in Vissian biology. Cogenitors are needed to complete the reproductive process: they do not genetically contribute to offspring, but supply an enzyme required for fertilization. Since cogenitors only constitute 3% of Vissian population, they provide reproductive functions to many different couples, and Vissians must apply to have a cogenitor assigned to them when they intend to conceive a child.
Tucker becomes increasingly intent on the rights of the cogenitor and seeks to visit the Vissian starship. He becomes more focussed when he visits his new friends' quarters and finds that the cogenitor does not seem to be treated well. It only eats one meal a day, rarely speaks, spends most of its time isolated in its room, and is not permitted to mingle socially. It does not even have a name; Tucker secretly runs some medical scans of it with the help of Dr. Phlox, and learns that cogenitors are actually as intelligent as any Vissian and could learn and grow as fast as anyone.
Meanwhile, elsewhere on the ship Lt. Reed finds himself the focus of a Vissian crewmember - their tactical officer, who quickly demonstrates that her interest in Reed is much more than professional. Similarly, Archer bonds with the alien captain whilst on a 3 day reconnaissance of the star in a small probe. On the alien vessel, without the couple's knowledge, Tucker secretly encourages the cogenitor to learn to read, while building a friendship with it. Despite having a near-total lack of education available, it is an insatiable learner. Soon learning the importance of names, it then asks be called Charles (Commander Tucker's own first name).
Charles soon realizes that "her" life in Vissian society would be unfulfilling; she then leaves and requests political asylum on Enterprise. Archer now returns to find himself in the middle of a diplomatic first contact crisis, with the Vissians confused and defensive at Tucker's interference in their customs. Tucker appeals to Captain Archer's sense of justice, but Archer sides with the Vissians. With the cogenitor returned, the Vissians hope good relations with the humans can continue. Later communications reveal however that the now despondent Charles has committed suicide, thereby delaying the birth of the Vissian couple's baby. Archer summons Tucker into his room and severely reprimands him for his lack of professionalism and judgment.