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".

Off-duty Japan Self-Defense Forces (JSDF) officer and otaku, Youji Itami, is on his way to attend a doujin convention in Ginza, Tokyo when a mysterious portal in the shape of a large gate suddenly appears. From this gate, supernatural creatures and warriors clad in medieval armor emerge, charging through the city, killing and destroying everything in their path. With swift actions, Youji saves as many lives as he can while the rest of the JSDF direct their efforts towards stopping the invasion. Three months after the attack, Youji has been tasked with leading a special recon team, as part of a JSDF task force, that will be sent to the world beyond the gate—now being referred to as the "Special Region." They must travel into this unknown world in order to learn more about what they are dealing with and attempt to befriend the locals in hopes of creating peaceful ties with the ruling empire. But if they fail, they face the consequence of participating in a devastating war that will engulf both sides of the gate. [Written by MAL Rewrite]

Several months have passed since the infamous Ginza Incident, with tensions between the Empire and JSDF escalating in the vast and mysterious "Special Region" over peace negotiations. The greed and curiosity of the global powers have also begun to grow, as reports about the technological limitations of the magical realm's archaic civilizations come to light. Meanwhile, Lieutenant Youji Itami and his merry band of female admirers struggle to navigate the complex political intrigue that plagues the Empire's court. Despite her best efforts, Princess Piña Co Lada faces difficulties attempting to convince her father that the JSDF has no intention of conquering their kingdom. Pressured from both sides of the Gate, Itami must consider even more drastic measures to fulfill his mission. [Written by MAL Rewrite]

Mido Ban and Amano Ginji are known as the Get Backers, retrievers with a success rate of 100%. Whatever is lost or stolen, they can definitely get it back. Despite their powerful abilities and enthusiastic behavior, Ban and Ginji are terminally broke no matter what they do simply because few people would actually desire to hire them. As a result, the pair of them tend to do dangerous jobs, often leading to unwanted re-encounters with their old (and dangerous) friends.