In 1960, the ruins of an American bomber were found in the Libyan desert, but the remains of the crew were never located. In Guerdon Trueblood's teleplay, the ghosts of a bomber crew hang around their derelict plane, awaiting the day that their bones will be recovered and given a decent burial. The sole survivor, navigator Russell Hamner, has in the intervening 25 years become a General. He joins an investigation team that has come across the wreckage, while the ghosts, headed by Major Devlin, plot to expose Hamner as a coward who deserted his post and left his crew mates to die.

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.

In 1944, Master Sergeant Robert Steven Savage was betrayed by one of his fellow soldiers, Krieger, a double-agent for the Axis Powers. He had Savage's entire squad killed and used him for various genetic experiments. Savage was then cryogenically frozen and sealed inside a secret bunker. 50 years later, G.I. Joe discovered the hidden bunker, Savage now has super-human strength, speed and agility and is in charge of the Screaming Eagles. Krieger is alive and known as General Blitz, leader of the terrorist organization the IRON Army. Sgt. Savage and his Screaming Eagles must stop him!

G.I. Joe faces a new enemy as an ancient society of snake people known as Cobra-La try to forcefully take back the earth from those who drove them underground eons ago.