Perhaps a small army of more advanced anti-mutant machines begin abducting mutants from the streets of Atlanta and are taken to be brainwashed. It eventually falls on the X-men to defeat the giant robots, the SH and find and rescue the prisoners. Perhaps even one of them could be captured to further fuel the X-team's motivations.
The background would be that a major underground kingpin, named Desmond, takes interest in the Atlanta area. He makes contact with the SH, deciding to test them as well as the newly formed X-men Atlanta branch. He sends some resources as well as someone to aid in the operation and keep an eye on them. The mission is to brainwash mutants and send them to be used as an ingredient of the enhancement drugs just released.
Since there are quite a few characters who were experimented on in research labs, there could be further development in regards to their story. This also gives more characters disconnected from the main story a chance to be involved in some way, either by helping the X-men or being captured/rescued. Also, the drug side-story could start as the precursor to his arc.
Though the plan ultimately fails, the kingpin has gotten what he wanted regardless.
