I did have, a long time ago, an idea for a sequel story where Jessie was the main antagonist, though her identity wouldn't have been confirmed until near the end since she goes by another name - Fuse. She survived the plate collapse, but her body and mind were broken in the process. Crippled, burnt almost beyond recognition, she lurks within a hidden lab deep beneath the ruins of Sector 7, not so far underground as to have had contact with DG, but enough that her presence would go unnoticed by any except those who knew what to look for.
Fuse would have been heard much more than seen, communicating with Cloud mainly by phone to give him the tasks she requires of him and keep him on the path she intends for him. She's consumed by the need for vengeance and rage at what his arrival ultimately brought about for her home and friends. Her desire is to punish him, personally and deeply, for the plate collapse even though he tried to stop it. In her maddened state, all she knows is that he failed, and she blames him for that. Yet at the same time, she's torn because she still holds a part of those old feelings she once had for him, a tiny bit of her old self that refuses to die along with the rest of it.
By working with Argento in the years since ACC and Dirge, Fuse has secretly amassed a small force, the remnants of Deepground that survived the battle in Dirge. She has no desire for conquest, only revenge, and her forces are more directed toward stealth and surveillance than combat and destruction. Fuse uses her forces, along with her considerable technical expertise and the array of tiny minicameras she's secretly constructed and deployed, to monitor Cloud and his family. She knows almost his every move, and she uses that knowledge to manipulate him into making a series of very special deliveries after her forces kidnap his children - Denzel, Marlene, and his new baby.
The deliveries involve certain components that he'll have to obtain from several of his old friends. Knowledge, materials, and devices that Fuse intends to use to accomplish her goal - the creation of a new, enhanced body capable of being a match for him and taking him down. Part of Fuse's revenge is in using him to help create the means of his own destruction. And she punishes his attempts to stop her or deviate from her instructions with several cunningly planted bombs - hence her chosen name of Fuse. Small at first, to serve as a warning, but steadily increasing in severity.
However, things don't go as Fuse plans. Argento eventually betrays her, using the enhancements on herself and leaving Fuse with a weaker, more human (but still somewhat enhanced) body instead. Cloud beats Fuse but doesn't kill her in spite of all she's done, knowing who she really is because she's revealed herself to him before the procedure to infuse her consciousness into the new body (hey, if Hojo could do it in Dirge, why not her, lol?). He ultimately finds a way to reach her, the real Jessie, and bring her back. And then they, along with the others, fight and beat Argento and save the kids.
