In 2371, Bashir proposed that the rebels destroy Terok Nor in order to prevent Jennifer Sisko from completing a transpectral sensor array which would reveal the rebels' hiding places in the Badlands. Bashir was surprised (to put it mildly) when Benjamin Sisko apparently returned from the dead; he immediately got into an argument with Sisko who promptly decked him. Bashir didn't realize at the time that it wasn't "his" Captain Sisko, but rather the captain's counterpart from "our" universe.
When Sisko returned to Terok Nor the following year to help the rebels complete construction of the warship Defiant, Bashir immediately hit Sisko as payback for getting punched the previous year.
Bashir and Jadzia were lovers; when the Alliance attack on the rebel-occupied Terok Nor was imminent, he and Jadzia took a raider and managed to delay the Alliance's assault by projecting a series of warp shadows to draw off the enemy fleet. After this successful diversion, Bashir returned just in the nick of time to help the Defiant finish off the Regent's flagship at the Battle of Terok Nor. Smiley was less than pleased at being grateful for Bashir's timely return.
When his lover Jadzia was killed during a skirmish with the Alliance in early 2375, Bashir became even more irritable and unreasonable. He personally shot and killed Vic Fontaine and wanted to torture Ezri.