Part 1
A couple of years later at age sixteen, Jess changed his name to Jess Mariano and is working to find and reunite with his parents and take down Striker and his division that took them. He also has huge trust issues and doesn't want to connect with others. He lives off the grid using his survival skills and ends up in Hartford based on a lead.
Rory and Jess first encounter each other at a book store. Rory sees and/or ends up with something that she shouldn't have, but she doesn't know it or that she's in danger. Jess begins to interact with her for information for his mission.
Logan eventually escapes, due to secret assistance from Rogue when she finds out where he was in the facility, and runs into the X-Men.
Rogue is captive and forced to use her powers for Striker, but she also subtly fights back and works to protect her loved ones. She is thought to be evil by others, who don't realize that she is a victim.