After Leader X is apparently destroyed for good at the conclusion of Gatchaman II, a surviving fragment of him grows and transforms into Z. Alongside the head of the Egobossler family, Count Egobossler (and his two underlings Mechandol and Kempler), Z is determined to destroy Earth and once again target the Science Ninja Team.
Following Anderson's death, Dr. Nambu becomes the new leader of the ISO, while the team is confined to the underwater base Gallatown (also called "G-Town"). Engineer Kamo is introduced, and after the New GodPhoenix is destroyed early on, the team receives the new Gatchaspartan as their mecha. The Gatchaspartan also has a special mode called Hypershoot, which only Ken can use (with his new "Gatchafencer" sword).
As the story progresses, it is revealed that the radiation exposure from frequent use of the Hypershoot is slowly killing Ken, and continued use would result in death. Meanwhile, Z plans to destroy Earth using an antimatter asteroid codenamed "Poison Apple."