In an alternate universe where the Dominion won the Dominion War, Winn held Bajor together after the lose of the Emissary of the Prophets and the darkening of the orbs. Following the Dominion's victory in the Unification War she spearheaded Bajor joining the Dominion. Through the negotiations she arranged for all the orbs currently held by the Cardassians to be returned to Bajor as well as an agreement for the Dominion not to station any troops on Bajor itself.
At the first Festival of Tears Winn had an orb experience were the Prophets told her not to dismiss Jake Sisko as he would have a role to play in Bajor's destiny. This led her to try to foster closer ties with Jake than she had with his father, which included presiding over his wedding to Korena, sending gifts for birthdays and always inviting him to attend the annual Festival of Tears.
After Jake had is own orb experience at the festival she gained him permission to enter the caverns of B'hala so he could pursue the path he saw in his vision.
Following the seizure of the Reckoning Tablet by the Dominion and its transport to Gateway Station Bajor started to suffer serious natural disasters, which were attributed to the tablet been removed from the planet. In response Winn travelled to the station to request it be returned. However, she was not successful and with the help of Kira Nerys convinced Jake to speak to the Weyoun and try to convince him to return the tablet.
Upon learning that Dukat was possess by the Kosst Amojan Winn went to confront him and try to convince him to turn his back on evil. Dukat was unimpressed and killed her close companion, Solbor, as a display of his power. Dukat refused to kill her and instead wanted her to witness the destruction of Bajor by the Pah-wraiths.
Winn was rescued from the promenade by Jake and Lieutenant Lenaris Nanpa. Lenaris was meant to evacuate Winn, but instead she made her way to the station's ops centre. There she explained to the station's commander, Colonel Antara Eri, that the Reckoning was underway and the danger to the station. She suggested for the station to be evacuated, which Antara agreed with.
When Weyoun attempted to interfere with the Reckoning Winn tried to stop him, but was easily pushed away. Weyoun was killed by Antara and the evacuation continued. Winn opted to remain on the station with Antara to oversee the evacuation.