Enforcer Teppei Sugou, former ace pilot of the National Defence Army's 15th Integrated Task Force, is visited by a scout from the Ministry of Foreign Affairs and invited to rejoin the military. While considering the offer, he recalls his last months of service. His last mission, Operation Foot Stamp, had been a highly classified military strike against the Southeast Asian Union. The operation quickly went south for the ground forces, and Sugou's First Guardian drone was ordered in as air support to drop emergency supplies for the ground units and then return to base. Following orders against his own judgement, Sugou abandoned his comrades on the field. Many lives were lost during the operation, including Itsuki Ootomo, Sugou's commanding officer. However, three months later, following a massacre at the Ministry of Defence, Otomo was spotted at the scene on camera. Now a suspect in an act of terrorism, Sugou cooperates with Enforcer Tomomi Masaoka and Criminal Investigation Department's Division 01 as they hunt his former mentor down.

Abandoned by their abusive parents and with only each other to depend on, siblings Utsutsu and Yume Hasegawa find themselves led astray by beautiful red butterflies that have appeared in their world. Unbeknownst to them, these crimson winged heralds trumpet the beginning of a cannibalistic nightmare—a mysterious virus known as Pupa is about to hatch. After succumbing to the full effects of Pupa, Yume undergoes a grotesque metamorphosis into a monstrous creature with an insatiable desire for flesh; Utsutsu, on the other hand, is only partially affected, gaining remarkable regenerative powers instead. Reaffirming the resolve to keep the promise he made to himself years ago, Utsutsu is willing to sacrifice everything in order to always be there for his precious little sister. Pupa tells the story of a loving brother's desperate struggles to save his sister while protecting the world from her uncontrollable hunger.

Ayato Kamina was separated from the girl he loved, Haruka Mishima, when an event occurred that was thought to have killed everyone outside of Tokyo. But one day three years later, invaders suddenly attacked the city. It was then that he meets an agent of TERRA, Haruka Shitow, who tells him that she will give him the truth about the world. It is the beginning of a series of strange events, which involve him activating a giant mecha, the RahXephon and finding out that many people, including his own mother, has blue blood, and that he was actually living in a self-encased dimension where time moves slower than that of the outside world. (Source: ANN)

The ordinary life of high school student Ayato Kamina is turned upside down when Tokyo is suddenly invaded by futuristic fighter jets. Amidst the chaos, he encounters a woman called Haruka Shitow who claims to be from a government organization called TERRA. She reveals that he has been living in a time bubble named Tokyo Jupiter that was put in place by the Mulians—humanoids from another dimension—in an attempt to isolate and take over Tokyo. TERRA has been trying to break through the barrier surrounding the city ever since. Unable to process the revelation, Ayato panics and flees. He runs into his classmate Reika Mishima who leads him to a place called The Shrine of Xephon where a large egg slumbers. She starts to sing and an unknown power awakens within Ayato, connecting him to a being called RahXephon that breaks out of the egg. Shortly after, Haruka finds him again and tries to make him join her cause of fighting against the Mulians. Caught between the crosshairs of the Mulians and TERRA, Ayato begins to question his purpose, navigating altered memories and ultimately his very identity in this chaotic new world.