After Leader X is seemingly destroyed for good at the end of Gatchaman II, a fragment of him that survived grows and mutates into Z. With the head of the Egobossler family, Count Egobossler (and his two subordinates Mechandol and Kempler), Z is bent on destroying the Earth, and the Science Ninja Team, once more. In the wake of Anderson's death, Dr.Nambu has become the new head of the ISO, while the team is now confined to the Gallatown (aka "G-Town") underwater base. Engineer Kamo is introduced, and after the New GodPhoenix is destroyed early on, the team receives the new Gatchaspartan as their mecha. The Gatchaspartan has a special mode as well, called Hypershoot, that can only be utilized by Ken (with his new "Gatchafencer" sword). As the series progresses, it is learned that the radiation exposure from constant use of the Hypershoot is slowly killing Ken, and that continued use would mean death. Meanwhile, Z plans to destroy the earth with an antimatter asteroid, codenamed "Poison Apple".

In a futuristic world, the Maruhage Empire is a militant organization out to steal everyone's hair, and thus their freedom. But a brave man with an afro of gold and nose hairs of steel stands up against their tyranny. Bobobo-bo Bo-bobo, trained in the ways of hair, rescues a teenager named Beauty from the grunts of the Maruhage Empire. Together, they start on a journey to defeat Emperor Tsuru Tsurulina IV. As Bo-bobo meets new friends and battles foes along the way, so too does he begin his quest to save all the hairs of the world! Light-hearted and comical, Bobobo-bo Bo-bobo details a wacky adventure in which Bo-bobo and his companions fight all sorts of villains and deviants within the Maruhage Empire, all the while having a fun and exciting adventure. [Written by MAL Rewrite]

Special Vehicles Division 2 is back on duty, along with their Ingram Patrol Labor (Patlabor) robots. Using their courage as well as the Ingrams, Captain Goto's motley crew of officers battle crime in Tokyo city. They also deal with their personal lives, as well as the supernatural. (Source: ANN)

The story follows a boy who was in a soccer team, but it was disbanded due to not enough players. However, after the boy meets a female professional soccer player, he aims to bring his soccer team back. (Source: AniDB)