Something I laid the foundations for, which would likely fit better for a sub-plot, is subliminal triggers. These triggers could have been laid while a mutant was at the research facility (such as what happened with Raphael). The triggers could be as simple as a safe-word that renders the subject unconscious, or possibly sends them into a berserk frenzy that keeps them from telling friend from foe, to possibly as complex as driving the subject to walk to a preprogrammed location.

As I said, maybe not a stand-alone plot, but it could be worked in just about anywhere to supplement another plot… especially if it involves a government agency (for Raph it is the group behind a top secret military project)….
Ideas?

Yea, I say go for it if you'd like to do that with Raphael. I'm for it!

I probably wouldn't mind too much if something like that were to happen to Jaya as well, she was in the research facility.