Season Three

In speculation of a Dominion attack, Starfleet stationed a new class of starship, the Defiant Class Defiant, at Deep Space Nine. After installing a Romulan cloaking device on board the ship, the senior officers of DS9 went into the Gamma Quadrant to locate the "Founders", the leaders of the Dominion. During the confusion of a Jem'Hadar attack Odo kidnaped Major Kira, stole a shuttlecraft, and went to the Omarion Nebula, to which he felt drawn for some reason he couldn't explain. They landed on a small planet where he and Kira located the Founders, and discovered that they were made of a transforming gelatinous substance just like Odo–he was really one of them! He was told by a Female Changeling that he was one of one hundred infant Changelings that were sent out to explore the galaxy. Meanwhile, Kira had detected a strange power source under the planet's surface. She and Odo found the other senior officers hooked up to a series of brain probes in an underground room. A Vorta explained that through the probes, the Dominion wanted to see how serious the Federation was about their peace claims. The officers learned that the Founders established the Dominion thousands of years ago to bring their sense of order upon a chaotic galaxy filled with "Solids" (people unable to change form like they could). The crew was let go, and Odo returned to Deep Space Nine with them, regretting that his people were so barbaric.

The Cardassians and Romulans were told what the Federation had learned about the Founders, and secretly organized a plan to destroy their home world. Garak (exiled from Cardassia during the Occupation, and the only Cardassian that continued to live on Deep Space Nine) joined the mission, and kidnapped Odo to bring him along as a source of information. Garak reluctantly used a torturing device to get Odo to admit he was torn between wanting to return to his people and staying with his friends in the Alpha Quadrant. The Cardassian-Romulan fleet of starships blasted the Founder's home world with phaser fire and quantum torpedoes, but the planet had been completely deserted. Months before, when the plan was in its infancy, a Changeling had replaced a Romulan leader and convinced the Romulans and Cardassians to go into the Gamma Quadrant so that the Jem'Hadar could easily attack their ships. The entire fleet was destroyed, but Odo and Garak were able to make it back to DS9 when the Defiant came through the wormhole to rescue them.

By the end of this season, tensions between the Dominion and the various Alpha Quadrants powers had rose to a point where the Federation's major task was to calm all developing wars. The Founders had been assuming the positions of various race leaders, thus trying to influence the Alpha Quadrant empires into wars with each other, so that the Dominion would easily be able to conquer the entire quadrant in its weakened state. In one of those attempts on the Defiant, after Commander Sisko was promoted to captain and Jadzia promoted to lieutenant-commander, Odo accidentally killed one of his own people--something which had never happened between Changelings--when a fight broke out near the warpcore.