After learning that both Elena and the members of Team Harlequin switched sides to join the Allied Forces, Ao and his friends manage to escape taking the Quartz Gun with them. With nowhere to run, the remaining members of Team Pied Piper are contacted by the Japanese government offering them shelter and support according to a deal Cristophe made with the Secrets before his death.
To protect his comrades, Ao surrenders himself, the Nirvash, and the Quartz Gun to the U.S. army. As the whole world questions about Generation Bleu's actions, Fleur and Elena decide to launch an attack on the carrier where Ao is being held to bring him back.
Ao confirms that the members of Team Goldilocks are leaving ordinary lives as if they were never assembled at all. However, the public opinion starts turning against Generation Bleu and during an operation in the middle of the ocean, the Quartz Gun starts moving by itself. Truth snatches the gun from Ao who falls into the sea and has a brief encounter with Eureka who revels to him the reasons for her disappearance.
Several countries join Generation Bleu's special operation to lure all Secrets that have appeared arround the world to a deserted area in the Arctic and destroy them. The plan goes well until Truth interferes and Ao takes the initiative to ensure that the operation ends with no civilian casualties.
Despite Truth's intervention, Ao manages to return Eureka to her proper time, but hears from her that the baby she is carrying is not a boy, but a girl. After returning home to find more about it, he learns from his grandfather that Naru reappeared, but upon reuniting with her, the Japanese government declares claim of Iwato Jima and blames Ao for the death of one of its officers.
On board the Gekko, Ao discovers that the Eureka before him is a past incarnation of her, from the time she was still pregnant. Soon the ship is surrounded by the Japanese and Okinawan armed forces, all desperate to take possession of both the past Eureka and her Nirvash. While trying to figure out how to send Eureka back to her own time, Ao and the others are attacked by Truth.
Team Pied Piper returns from a mission in Australia, unaware that they had brought with them a sand-like substance that makes the child pilots have strong hallucinations. Meanwhile Gazelle and his friends investigate the past of Ao's fellow pilot Elena Peoples just to discover that she is even more mysterious than they previously imagined.
A Scub Burst appears in Phoenix, Arizona and while Team Pied Piper is on standby waiting for an official authorization to intervene, Ao and Ivica get ahead to evaluate the situation. As they arrive there, Ao meets Truth once more, holding a group of survivors hostage while the US Army comes with a different approach to confront the enemy secret with disastrous consequences.
The Japanese government runs an experiment on Tokyo Bay trying to create its own Plant Coral. However, a Secret appears and starts wreaking havoc. Team Pied Piper is dispatched to the area, but when Ao is informed that protecting the city from the Secret is not their top priority, he leaves against orders to engage it.
A Secret appears in the Republic of Faisal Arabia, but on behalf of its interests, the United States government exerts its pressure on Generation Bleu to not engage it. Ao's comrade Fleur Blanc reveals to him the reason why she hates her father, Generation Bleu's president Christophe Blanc. Ao manages to cheer her up and both return with renewed spirits to battle when they are finally authorized to confront the enemy.
The stranger, who names himself "Truth" invades Generation Bleu's headquarters in search for the Nirvash. After having a confrontation with him, Ao is knocked unconscious and dreams about Truth approaching Naru and disappearing with her. After waking up, Ao is informed that Truth was indeed at Iwato Jima and took Naru away.
While adjusting to life on Generation Bleu, Ao begins to feel uncertain about why he joined them in the first place. Meanwhile, Team Goldilocks is under attack during an operation.
With renewed resolve to protect Iwato Jima, Ao takes on the G-Monster with some help. And in the aftermath, Ao begins to learn that the world is more complex than he realized. In hopes of finding his mother and learn more about his birth, Ao decides to join Generation Bleu.
The G-Monster continues its attack on Iwato Jima, and with Gazelle's help Ao pilots an IFO being transported by the Japanese Navy and uses it to defeat the G-Monster, his hair changing color to turquise in the battle, all while Team Pied Piper pilots watch, realizing that the IFO is the first ever model made.
Renton Thurston desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure. When a robot crashes through Renton's garage the meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside the young girl Eureka as the co-pilot of the Nirvash.