Odo is rushed to the Infirmary when he suddenly collapses. After a thorough examination, Bashir determines that Odo is losing the ability to maintain his solid form, but it is unclear as to why. Despite his protests, Bashir gives the patient strict orders to remain under observation since movement could bring on another attack. Odo reluctantly consents, until Kira brings him the day's criminal activities report to take his mind off his troubles. He sees a suspicious notation, leaves the Infirmary to investigate, and promptly collapses into a puddle of goo.

His condition worsening, Odo realizes there is only one place he can find help — with his people, the Founders. Sisko, O'Brien, Worf, Bashir, Dax, and Garak take him into the Gamma Quadrant on the Defiant to find his mysterious homeworld. Soon, the Defiant, is intercepted by a squadron of Jem'Hadar warships.

Three Jem'Hadar warriors and the Female Shapeshifter who confronted Odo in the past materialize on the bridge. She has come for him, stating that only returning to this homeworld's Great Link can help him, and takes over the ship's navigation controls to keep secret their destination. She then meets with Odo and is able to stabilize his condition temporarily by linking with him. He then realizes that the Founders caused his illness to force him to return. As the only Changeling to kill another of his kind, Odo has been brought back to be judged by his own people.

The Female Shapeshifter explains that Odo must rejoin the Great Link, not only to be cured of his illness, but in order to allow his people to determine whether his actions were justified, and what punishment should be given. Sisko and the others try to develop a plan to protect Odo, but he tells them that he wants to be judged. Upon arrival at the homeworld, Sisko and Bashir transport to the surface with Odo and the Female Shapeshifter, then watch helplessly as the Changelings disappear into the sea of goo that is Odo's people — joined in the Great Link.

On the Defiant, Worf catches Garak attempting to fire the ship's weapons on the planet, refusing to help him commit genocide on the Founders and kill Sisko, Bashir, and Odo in the process. Later, Odo is expelled from the Great Link — as a human. The Female Shapeshifter explains that this is their punishment, but left Odo's face as it was to remind him of what he lost. Soon after returning to the station, a message from Gowron, leader of the Klingon Empire, is received. As the crew watches what borders on a declaration of war against the Federation, Odo reaches a startling realization. Gowron is not a Klingon at all. He is a Changeling.