Galactor's missiles destroy the Coral base. Ken and Jun are inside with Dr Nambu. The God Phoenix has to return to try and salvage anything from the remains of the base.
Condor Joe pays a secret visit to the island where his parents are buried. An agent of Galactor spots him and alerts Katse who plans to stop Joe ever leaving the island.
The team set out to thwart a new Galactor attack but Dr Nambu and Joe are nowhere to be found. Nambu has been hidden away digging up clues about Katse's true identity.
Galactor blows up an ocean liner full of scientists. When the Science Ninja Team show up to investigate the wreckage, Katse plants a tracking device on the God Phoenix so he can find the location of their coral base.
Gatchaman finds Katse's old school reports, but every alternate year is missing. A visit to Katse's old school reveals some interesting clues about his true identity.
Ken escorts an important scientist on a flight, but they soon discover the plane has been sabotaged. A crash landing leads Ken and the scientist into a whole new world.
Earth is moments away from destruction. Gatchaman has to find the entrance to Galactor's secret base to stop Leader X and Katse from completing their dastardly plan.