Aboard space station Deep Space Nine, Constable Odo suddenly collapses, and is taken to the Infirmary. Chief Medical Officer Dr. Bashir performs an exam, and determines that Odo can no longer maintain a solid form, but Bashir can't find an explanation as to what is happening to Odo. The only thing Bashir can do is to give Odo medical orders to remain under observation and to take a rest from his duties. Odo is reluctant do so, but decides to obey the doctor's orders for the time being. Kira stops by, and brings him a report of the day's criminal activities. She hopes that this will take his mind off what is happening to him. While reading the report, he notices something that catches his eye. He then attempts to leave the Infirmary to investigate. He doesn't make it far, and loses his shape and collapses into a puddle on the floor.
Odo then comes to the realization that the only people that can help him are his own people, the Founders. With the help of Captain Sisko, Commander Worf, Dr. Bashir, Lt. Dax, and Elim Garak, Odo is taken to the Gamma Quadrant aboard the starship Defiant. They are met by the Female Shapeshifter and three Jem'Hadar soldiers. The Female Shapeshifter tells Odo that the only way he can be helped is by coming with them to join with the Great Link. The Jem'Hadar soldiers then pilot the Defiant to the location of the Great Link, using a device to keep the location of the Great Link a secret. Later on in his quarters, the Female Shapeshifter visits Odo, and by linking with him she is able to temporarily stabilize his condition. Odo quickly comes to the conclusion that he was somehow infected by the Shapeshifters in order to force him into returning to the Great Link. He also learns he is to be judged by the Great Link, as he is the only changeling to have killed another of his kind.
The Female Shapeshifter tells Odo that he must join the Great Link not only to be cured, but to also let the other changelings know why he killed another of his kind. She tells him that the Founders have infected Odo with the disease, but in a later episode we learn that this isn't true. Odo is also told that while he is in the Great Link, he will be judged by the other changelings, and that at the same time his punishment will be determined. Sisko and his crew try to protect Odo, but he tells them he wants to be judged. As a man of justice all his life, he feels that he is not above justice himself. Afterwards, Garak asks the Female Shapeshifter if there are any Cardassian survivors from the failed Cardassian-Romulan attack on the Founders' homeworld a year earlier. She bluntly replies there were no survivors. Sisko and Bashir then accompany Odo and the Female Shapeshifter to the surface of the planet they are orbiting. Once on the surface, a small island in a sea of Changelings, they realize how many Changelings there are. And as far as they can see it is a sea of Changelings in their liquid form, even from orbit the planet appears to be covered by Changelings in their liquid form. Odo and the Female Shapeshifter then walk into the sea, leaving Bashir and Sisko to wait for them.
On the Defiant, Worf catches Garak attempting to fire the ship's weapons on the planet, and stops him from committing genocide on the Founders and killing Sisko, Bashir, and Odo in the process. Back on the surface, time goes slowly and Bashir in his boredom nearly throws a rock into the Great Link, but is stopped just in time by Sisko. Later, Odo is expelled from the Great Link — as a human. The Female Shapeshifter explains that this is Odo's punishment, but the Founders 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 has been replaced by a Changeling.