Throughout the pilot episode "Emissary", Benjamin is still struggling emotionally over Jennifer's death and the pain of her loss causes him to consider resigning from Starfleet. It is not until his first encounter with the aliens residing in the Bajoran Wormhole - one of which assumes Jennifer's form - that Benjamin finally comes to terms with Jennifer's loss and learns to move on.
Mirror UniverseThe mirror counterpart of Jennifer Sisko first appears in the third season episode "Through The Looking Glass". She is a Terran scientist who is forced by the Klingon-Cardassian Alliance to develop a trans-spectral sensor array that will help the Alliance route out the Terran rebels hiding in the Badlands. She never finishes her project as she is rescued by the prime universe counterpart of her late husband Benjamin.
A year later, in the episode "Shattered Mirror", Jennifer visits the prime universe and approaches Captain Sisko's son Jake. Jake is enraptured by this woman who so closely resembles his dead mother and follows her back to her universe, which Jennifer had planned in order to lure Benjamin back to help her and the Terran Resistance complete the construction of their own version of Sisko's ship, the Defiant. Unfortunately, the malevolent Intendant Nerys, who was held captive on Terok Nor, escapes confinement and runs into Jennifer and Jake in a corridor as she makes her way to a docking pad. In order to hurt Captain Sisko, Nerys decides to shoot his son, but Jennifer throws herself in front of Jake and takes the phaser hit. Even though Jake is not her son, Jennifer still feels a strong bond with him and was willing to sacrifice herself for his safety. She later dies from her wound as Benjamin and Jake weep over her.