After yet another defeat inflicted by G.I. Joe, the immediate subordinates of Cobra's leader, Cobra Commander, have finally come to the end of their patience with his apparent incompetence and his inability to achieve real victories. The leader of the research and interrogations wing, Dr. Mindbender, receives a dream showing the solution. His plan is to collect the genetic material of great warriors and military leaders to create a composite clone that would be the perfect leader for Cobra. Now they set out to put this scheme into motion, and G.I. Joe has very little time to learn of this plot before Cobra becomes that much more a dire threat to the world.

After a senator suddenly dies after completing (and sealing) an investigation into the nuclear power industry, the remaining senator and the state governor must decide on a person who will play along with their shady deals and not cause any problems. They decide on Billy Jack, currently sitting in prison after being sent to jail at the end of his previous film, as they don't expect him to be capable of much, and they think he will attract young voters to the party.

Action-packed cartoon feature about the age-old fight between good and evil. Mysterious events start to happen when the government Earth Corps unearths an amber monolith in a forest; meanwhile, an unscrupulous businessman, Blackthorn, digs up a vine creature, Tendril, which frees the trapped undead beast, Decompose. Earth Corps must use their specially-designed armoured suits to track down the enormous monsters. In the process, the dormant Mutar species of Redwoods, Granites and Magnacore are reawakened, and join forces with Earth Corps to once again do battle with their centuries-old enemies, the Inhumanoids, in an effort to save the world.