After Leader X appears to be destroyed completely at the close of Gatchaman II, a surviving fragment of him mutates and evolves into Z. Joined by Count Egobossler, the head of the Egobossler family, along with his lieutenants Mechandol and Kempler, Z is determined to destroy Earth and once again eliminate the Science Ninja Team.
Following Anderson's death, Dr. Nambu takes over as the leader of the ISO, while the team is now stationed at the underwater base known as Gallatown (or "G-Town"). A new engineer named Kamo is introduced, and after the New GodPhoenix is destroyed early on, the team receives the Gatchaspartan as their new mecha. The Gatchaspartan also features a special mode called Hypershoot, which can only be accessed by Ken using his new "Gatchafencer" sword.
As the story progresses, it becomes clear that the radiation exposure from repeatedly using Hypershoot is gradually killing Ken, and any further use would result in death. Meanwhile, Z plots to annihilate Earth using an antimatter asteroid codenamed "Poison Apple."