Odo suddenly collapses, having difficulty maintaining his form, and is taken to the infirmary. Dr. Bashir cannot find an explanation for Odo's condition, but advises him to take a rest from his duties. Odo is reluctant to do so, but when he leaves the infirmary to investigate a crime, he collapses into a puddle on the floor.

Odo knows that the only people that can help him are his own people, the Founders of the Dominion. Captain Sisko agrees to take Odo to the Gamma Quadrant aboard the Defiant; the Cardassian spy-turned-tailor Elim Garak asks to come along as well. They are met by a spokesperson for the Founders, who tells Odo that the only way he can be cured is by physically joining the Founders in the Great Link, where he will be judged for the crime of being the first Changeling to harm another. Odo surmises that the Founders themselves must have infected him in order to coerce him into returning to the Great Link. A squad of the Dominion's Jem'Hadar soldiers accompanies the group aboard the Defiant, navigating to the Founders' planet and erasing all records of the journey from the ship's computer.

Garak asks the Founder if there are any Cardassian survivors from the failed Cardassian–Romulan attack on the Founders' homeworld a year earlier. She bluntly replies that there were no survivors and that Cardassia is doomed. Later, Garak attempts to fire the ship's weapons on the Founders' planet and annihilate the Changelings, but Commander Worf catches him and stops him.

Sisko and Bashir accompany the Founder and Odo to the planet and see the Great Link: a sea of Changelings in their liquid form. Odo and the Founders' spokesperson walk into the sea, leaving Bashir and Sisko to wait for them. Eventually, Odo is expelled from the Great Link; Bashir notes in astonishment that Odo's body has become human. The Founders' spokesperson explains that this is Odo's punishment.

After they return to the station, a message from Gowron, leader of the Klingon Empire, is received, declaring the initiation of hostilities against the Federation. Watching the message, Odo reveals that he felt that the Founders were trying to hide information from him while he was in the Great Link, but now he thinks he knows what it was: Gowron himself has been replaced by a Changeling.

The episode is a turning point in the story arc of Deep Space Nine, having many plot connections to other episodes:

• The failed Cardassian–Romulan attack on the Founders, led by Garak's father Enabran Tain, was depicted in the third-season episode "The Die is Cast".
• In the third season finale, "The Adversary", Odo killed another Changeling that was attempting to take control of the Defiant, leading to his punishment by the Great Link in this episode.
• In the first episode of the fifth season, "Apocalypse Rising", Sisko and his crew attempt to unmask Gowron as a Changeling.
• In the fifth season's "The Begotten", Odo regains his shapeshifting abilities when he absorbs a dying Changeling infant.
• The fifth-season episode "In Purgatory's Shadow" reveals that the Founder lied to Garak in this episode; some Cardassians did survive the attack on the Founders, including Tain.
• Odo returns to the Great Link in the series finale, "What You Leave Behind", in order to cure them of a disease they were infected with by Federation machinations.

In 2019, Tor.com noted this as an "essential" episode for the character of Odo, remarking how it presents the character with major problems that are resolved in later seasons.^[2]

• "Broken Link" at IMDb  
• Broken Link at Memory Alpha
• "Broken Link" at Wayback Machine (archived from the original at StarTrek.com)