A.D. 2089 - 80 years have passed since Space War I changed the lives of both human and Zentraedi races. Both races are at peace on Earth when a new alien race called the "Marduk" appear within the Solar System. While covering the first battle between the U.N. Spacy and the Marduk fleet, SNN rookie reporter Hibiki Kanzaki discovers Ishtar, an "Emulator" that enhances the Marduk's combat abilities through singing. Hibiki brings Ishtar to Earth to teach her the values of life and culture. Together with ace Valkyrie pilot Silvie Gena, Hibiki and Ishtar must find a way to save Earth from total destruction at the hands of the Marduk leader Ingues.

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".

​Like many in her class, Koyuki Honda looks forward to her graduation ceremony. However, while her peers have family to attend, Koyuki has no one, as her only family—her brother—died years ago. While visiting his grave, she meets two brothers named Kiri and Victor Putin chasing a strange creature. They try to assure her that they are just actors shooting a movie; Victor, however, piques Koyuki's curiosity about the old legend of the clock tower at the cemetery: if you make a wish under the clock tower at midnight during a full moon, time will turn back, allowing someone to reclaim what they have lost. Deciding to make her wish, Koyuki learns the horrifying truth: the legend is a ruse for time demons called "Horologues" to steal humans' time. As they are drawn to regrets, Victor uses Koyuki as bait to lure a demon there. Kiri and Victor explain that they are Chronos Rulers, warriors who fight against the Horologues using the "Oath of Time"—an item allowing them to speed up or slow down time. With the demon destroyed and the crisis averted, Koyuki is able to go on her way free from regrets. However, she is not the only human with sorrows. The two boys must continue to hunt down Horologues in order to keep humanity safe. [Written by MAL Rewrite]

Now there's a mysterious Mask before James Blood, and the man behind it is one that shouldn't exist. What is the mystery surrounding this mask...? So begins an action-packed crime story set in a beautiful city!