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".

Two years after the defeat of Galactor and the apparent death of Condor Joe, a cruise ship is attacked by Leader X, killing nearly everyone on board. One of the survivors, a young girl, is captured by X and rapidly aged into the bizarre, masculine-voiced villainess Gel Sadra. Though she has the appearance of an adult, Gel Sadra is not immune to throwing childish tantrums and behaving immaturely. In the midst of the revival of Galactor, the Science Ninja Team is called back into action, with a shady man known as Hawk Getz acting as the replacement for Joe. Getz is quickly revealed to be a Galactor agent in disguise (and had killed the actual Getz who was to join), and winds up killed by a mysterious feather shuriken. After hints spread in the first three episodes, Joe reappears in the fourth episode, having somehow survived his fatal injuries at the end of the first series, and rejoins the team. It is later revealed that he was rescued by an ex-Galactor scientist at the brink of his death, and was the subject of various cybernetic augmentations. Later in the series, a female scientist known as Dr.Pandora is introduced, who had lost her husband and daughter in the cruise ship disaster. Unbeknown to her, her daughter Sammie survived and is in fact Gel Sadra.

In a tranquil neighborhood of Tokyo, seven students are avoiding going to school—hiding in their darkened bedrooms, unable to face their family and friends—until the moment they find the mirrors in their bedrooms are shining. At a single touch, they are pulled from their lonely lives into a wondrous castle straight out of a Grimm's fairy tale. This whimsical place, oddly lacking in food and running water but full of electrical sockets, is home to a petulant girl in a mask, named Wolf Queen and becomes their playground and refuge during school hours. Hidden within the walls, they're told there's a key that will grant one wish, as well as a set of clues to find it. But there's a catch: the key must be found by the end of the school year and they must leave the premises by five o'clock each day or else suffer a fatal end. As time passes, a devastating truth emerges: only those brave enough to share their stories will be saved. And so they begin to unlock each other's stories: how a boy is showered with more gadgets than love; how another suffers a painful and unexplained rejection, and how a girl lives in fear of her predatory stepfather. As they struggle to abide by the rules of the game, a moving story unfolds, of seven characters trapped in a cycle of misunderstanding and loneliness, who are ultimately set free by the power of friendship, empathy, and sacrifice.

Kagemori Mamoru is a dowdy boy whose hair is disheveled and who wears thick glasses, but he is actually the son of a ninja family. They have protected their neighbors, the Konnyaku family, secretly for 400 years. Mamoru has personally protected their daughter, Konnyaku Yuuna, since they were in kindergarten. When Yuuna is in trouble, Mamoru puts on ninja suit and turns into a competent ninja to help her.