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.

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.

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 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.

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.

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.

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.

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.

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.

April 2025. While helping his childhood friend Naru Arata, Ao Fukai accidentally takes a bracelet being smuggled by Gazelle, Pippo, and Han Juno, and a Scub Coral suddenly appears, along with a G-Monster. Gazelle and his friends were smuggling the item to the Japanese Armed Forces, but they discover the bracelet is missing and go to find Ao to try to retrieve it. In the interrim, another Scub Coral and G-Monster appears, as Cristophe Blanc of Generation Bleu makes a deal with the Union of the Okinawa Islands government to take care of the new G-Monster. Ao soon realizes that the bracelet is one owned by his mother years ago, just as Gazelle goes to take it back.