Quick recap
The series picks up Marvel's numbering as if the stories other publishers released later never happened. The G.I. Joe team has been disbanded, and Cobra wins the contract for homeland security in a terror-stricken United States. Behind the front, its first order is to quietly kill off the former Joes. Snake Eyes responds in his own way, and the group regroups to hit a Cobra base. The raid works, but Scarlett and Snake Eyes are left behind. Storm Shadow brings Scarlett back to her teammates, who don't trust him or her state of mind, and the volume ends with Cobra trying to brainwash Snake Eyes.

