Jesse Pinkman is super loyal to the Initiative. If you're against them, he's against you. But he loathes violence and would rather avoid it, so he's going to be disarming people. As in, taking powers away from mutineers. You can read more about how this works here. At the end of the plot, when he's satisfied that fighting won't immediately resume, he'll return those powers to their rightful owners.

Please let me know if you want Jesse to peacefully disarm your character! (Your character may not even notice he's done it until he's already gone.)

Also let me know if you want a chance to get back at Jesse or take him down! Bullets usually do the trick just fine, though it's about time for him to evolve, so I might have something special in mind, depending. Anyway, we can plot a thing.