During an attempt to take down one of the occupied Forts, Connor is wounded and captured by the Templars/Redcoats. Instead of killing him, they decide to keep him (whatever reasoning you want - death is too good for him, etc). His recruits know something has gone wrong when they don't hear from Connor, and begin to search for him. They are unsuccessful, and after weeks of nothing, begin to lose hope that Connor is alive. As the weeks turn to months, the Assassins are forced to call the search off, and one of the others takes up leadership of the group.

Some more time passes, and after liberating a Fort from Templar/Redcoat control, one of the recruits finally finds Connor hidden away in a concealed room. He was clearly tortured (sexually or not), and the recruit is horrified at how broken/hurt the young man is (Connor reacts badly to touch when they try to help, doesn't realize/remember who they are, etc). They manage to get him to a safer, more secure area and hope that he'll recover soon, taking turns helping/watching over him (or they take him back to Davenport, where the homesteaders can help with his healing?)

It isn't necessary that Connor is fully healed in the end, the set up makes for years of healing before that happens. And I'm not looking for explicit torture scenes, but brief flashbacks when Connor is healing would be welcome. (I don't know about the rest of you, but I'm a sucker for h/c fic.)