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By 2377, she was married to Jaro Essa and, along with him and Opaka Sulan, was a member of the leadership triad of the Bajoran dissident movement enclave in Vekobet in the Kendra Province of Bajor. The enclave was passed off as a labour camp in which the vital metal uridium was processed by slaves. In reality, the slaves, who were composed of Terrans as well as Bolians and Tellarites, were agents of the dissident movement, as were their supposed Bajoran masters. Vekobet boasted rich veins of uridium, meaning that the enclave regularly exceeded the Alliance quotas. The excess uridium was transported to their allies elsewhere on Bajor. Winn posed as one of the camp's slave overseers while her husband posed as the camp's physician and devoted much of his time to caring for Vaughn, who had then was a blind and extremely frail centenarian who was confined to a hospital bed. Jaro was assisted in doing so by Vaughn's daughter Prynn Tenmei.
In January of that year, Vaughn's primary universe counterpart Commander Elias Vaughn and his superior officer Captain Kira Nerys made contact with the enclave and warned that the Iliana Ghemor of their universe was planning to discover the Bajoran wormhole and become the Emissary of the Prophets. Shortly afterwards, Klingon forces from the IKS Negh'Var launched an attack on Vekobet. Recognising that he would slow down Prynn and the other dissidents, he asked his counterpart to kill him. Commander Vaughn did so by shooting him with his phaser, which led to Prynn physically attacking him.
During their captivity on Terok Nor, which had recently been retaken by the Alliance, Winn and Jaro told Commander Vaughn that they understood why he had killed his counterpart and that they forgave him for doing so. However, Commander Vaughn doubted that Prynn would be as forgiving. With the assistance of the Jem'Hadar Taran'atar, Winn, her husband and their fellow dissidents were freed while Terok Nor was recaptured by the Defiant with support from a fleet of the Talarian Republic vessels. Winn and Jaro subsequently returned to Bajor. (DS9 novel: The Soul Key)
After the Iliana Ghemor of the mirror universe became the Emissary of the Prophets, the Bajoran people converted to their long neglected religion en masse and the senior members of the underground religious movement came out of seclusion to reconstitute the Vedek Assembly for the first time in centuries. Several weeks later, Opaka was elected as the Kai of Bajor while Winn became a vedek. With the destruction of the Bajoran Parliament in Ashalla and the consequent death of First Minister Li Nalas, the Vedek Assembly became the de facto government of Bajor with Kai Opaka as its leader. The Kai used her new-found authority to have Bajor secede from the Alliance and turned over all of the dissident movement's stored munitions to the Terran Rebellion aboard Terok Nor. In response, Supreme Legate Skrain Dukat sent the Cardassian Ninth Order to destroy Terok Nor and conquer Bajor. Although Terok Nor was destroyed, the Ninth Order was defeated through the telepathic manipulation of the Vulcan slaves within the Cardassian Union.
In 2378, after the joint Terran Rebellion / Memory Omega fleet succeeded in stopping the Klingon renegade Krona from destroying Bajor's sun B'hava'el, Vedek Winn and Kai Opaka met with its leaders Miles "Smiley" O'Brien, Jean-Luc Picard and M'k'n'zy of Calhoun in the Elemspur Monastery in the Hedrikspool Province. (ST - Mirror Universe novel: Rise Like Lions)