While Flint, Lady jaye, and Heavy Duty lead an operation to find an enemy they thought was dead, Snake Eyes, Storm Shadow, and Billy face the Arashikage clan's greatest threat yet.
First, it looks as though team member Scarlett is switching sides and going to Cobra. Then, Megatron and Cobra Commander are up to no good in a cross-over story with the Transformers, and some of the Joes' early careers and lives are revealed.