The story takes place in an alternate reality based in the year 1996, where humanity is advanced enough to develop long-range space travel, as well as bases on both the Moon and Mars. However, the Cold War tensions between the United States and the Soviet Union have not ended; rather, they've escalated as both sides build military facilities in space, and the shadow of nuclear conflict looms over humanity, both on and off Earth. Meanwhile, on the Red Planet, an exchange program created by the United Nations to promote peace and understanding is about to begin; the "Cosmic Culture Club," consisting of 16 boys and girls, as well as their instructor Elizabeth, arrives at the UN Mars base. Among the passengers is Anna a 14-year-old girl who serves as the narrator for the story. Suddenly, four unidentified humanoid robots classified as Super Powered Tracers are detected, engaged in fierce combat with each other. The UN base is caught in the crossfire and quickly destroyed, killing all but six members of the "Cosmic Culture Club"—Elizabeth, Arthur, Roan, David, Simone and Anna, and leaving them stranded on an inhospitable planet that has suddenly become a battlefield. As the battle ends, the lone SPT standing lands next to the terrified group and opens up revealing a pilot, who simply announces to them, "Earth is at stake."

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)