Ao is hunted down by the people of Iwato Jima because they still believe that he and his mother are to blame for the terrible accidents that befell the island when she appeared out of nowhere. While in the custody of local musician Kazuyuki Kinjo, Kinjo apologizes to him for what his generation has done, just as Ivica Tanovich of Generation Bleu seeks him out, realizing he is the pilot of the Nirvash. While Rebecka tries to convince the Okinawa Self Defense Forces to allow Team Pied Piper to get rid of the Scub Coral, another massive Secret appears to attack. Gazelle frees Ao who brings the boy back to the Nirvash, which he realizes must be the IFO piloted by his mother Eureka, and that he was the one meant to pilot it in her absence.

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.

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.

Team Pied Piper is dispatched to aid Team Goldilocks, but upon their arrival, they find that their leader sacrificed himself to save his companions. After retrieving the pilots and their IFO, they return to confront the enemy Secret leaving an exausted Ao behind. After awakening, Ao hears from Chloe, one of Goldilocks' pilots about their battle with the Secret and comes with a plan to defeat it. While Ao confronts the Secret, he is watched by an enigmatic figure who takes an interest to him.

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.

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 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.

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.

Team Pied Piper goes to a Generation Blue Space Station to deposit the collected Quartz. While there a Secret attacks a Scub Coral that materialized in low orbit, and Pied Piper is sent out to intervene. Meanwhile, Truth begins to set his plan in motion, and Gazelle and his friends investigate the area beneath Generation Blue HQ, discovering the Coral Relic. When Ao manages to destroy the Scub Coral in orbit, it turns out to have the Gekko inside of it with the Nirvash Type0 piloted by Ao's mother Eureka.

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.

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.

Wondering about Eureka's claim that the Secrets are not enemies, a sleep-deprived Ao is sortied along his team to confront a Secret which has appeared beside a Scub Coral that was mysteriously reactivated. Ao is shot down by the enemy and after waking up, he learns that the other Scub Corals arround the world are being reactivated, too, putting Generation Bleu in a state of maximum alert to confront the multiple Secrets emerging near them.

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.

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.

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.

Furious upon hearing that he is actually a Secret who lost his memory, Truth destroys Generation Bleu's space station among thousands of satellites around the globe. The Allied Forces blame Generation Bleu for the incident and launch an attack against them. Truth takes the opportunity to infiltrate the base and attempts to steal the Quartz Gun, but is stopped by Cristophe who sacrifices himself to allow Ao and Fleur to escape.

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.

Team Pied Piper, the Japanese Government and the Secrets join forces to prevent the Allied Forces from claiming the Scub Corals' Quartz. While Naru rallies supporters for her cause of having the Plant Corals shut down. Elena joins the Allied IFO squad along Maggie Kwan, but Eureka appears before them and makes Elena remember the truth about her origins that she wants so much to deny. Soon after, both are dispatched to fight Ao, and when he manages to finally dissuade Elena, Truth appears before them.

Truth attacks Ao who is rescued by Naru when he teleports him and the Nirvash to her side at Okinawa. Reunited once more, Ao and Naru discuss the situation when Team Harlequin appears and reveals that Truth's current form is affecting all people infected by the Scub Corals and for being the son of a Coralian, Ao should stay away from him. Regardless, Ao decides to join his companions against Truth. Meanwhile, back at Eureka's timeline, her husband Renton boards the original Nirvash in an attempt to rescue her.

Truth and Ao fight for the Quartz Gun until it fires once more, erasing Truth and converting Ao's Nirvash into the "Nirvash Neo". It also rewrites history once more to render it like Generation Bleu defeated the Allied forces including Naru. As Naru is being hospitalized, Ao witness the Nirvash Spec V3 coming from the pillar and comes at its encounter, meeting his father Renton for the first time.

After having a brief encounter with the phased-out Eureka, Renton sets with Ao to Iwato-Jima where he thanks Toshio for taking care of his family and then decides to make use of the Quartz Gun to destroy the original Scub Coral at his timeline and prevent it from spreading itself throughout the dimensions. As Ao confronts him to stop it, he learns that surprisingly, Truth has not fully disappeared, but has become the Nirvash Neo's archtype instead. Ao then decides to make use of the Gun's last shot to change Eureka's fate and have her reunited with Renton. Because of it, Ao is transported to the year 2027 where he bids farewell to Truth and returns to Iwato-Jima to resume with his life, despite the fact that there's a chance that no one in the world remembers about him anymore.