Una nueva actualización del juego trae consigo muchas novedades, entre ellas una misión secreta. Hiroto, casi sin querer, se ve forzado a participar en ella.

Los chicos creían que la misión ya había terminado y esperaban recibir sus recompensas, pero parece que todavía no han terminado del todo.

Pese a las reticencias de algunos aldeanos, Hiroto y compañía lucharán para defender la aldea del asedio de los Uniojos.

Believing that Freddie's mission is an ongoing story mission newly added to GBN, the four decide to continue the adventure. Freddie introduces them to members of the Resistance, who tell the Build Divers about their planned counterattack operation. The next task is a diversionary mission to support an attack on the One-eyes' giant base in the desert.

On the day of the operation, Parviz is late to arrive. Lamenting his previous incompetence, he tells the other Build Divers that he wants to quit. Kazami desperately tries to stop him, May is calm, and Hiroto is excessively realistic. Parviz remains determined, but then he is forced to begin the mission against his will.

While Parviz experienced great growth in the previous mission, Kazami alone is resentful at his own inability to distinguish himself. Meanwhile, the Build Divers head for the Resistance base where Freddie's brother Jed is stationed.

Though Gojo has asked him to look after Kazami, Hiroto is unable to figure out Gojo's real motive. And Kazami, unable to find a way to lessen the huge gap between his own ideals and his current state, can only agonize in vain. With their teamwork in this hazardous state, an escort and evacuation begin.

Hiroto and Kazami have made a small but very important improvement in their relationship. However, the Build Divers and the Resistance are now overwhelmed by the attack of the mysterious Gunpla known as "Seltsam." The pendant that Muran entrusted to Hiroto and the others seems to become a key to turn the tide, but… Meanwhile, May begins gathering intelligence at Magee's bar.

Hiroto and Kazami have made a small but very important improvement in their relationship. However, the Build Divers and the Resistance are now overwhelmed by the attack of the mysterious Gunpla known as "Seltsam." The pendant that Muran entrusted to Hiroto and the others seems to become a key to turn the tide, but… Meanwhile, May begins gathering intelligence at Magee's bar.

May's Wodom Pod has been destroyed while shielding Hiroto from an attack, and from it emerges May's mobile doll form. May is an EL-Diver, an electronic lifeform born from GBN itself. As the other Build Divers react with amazement, Mobile Doll May takes the offensive against the Gundam Seltsam.

The Space Crossing festival is over, and the Build Divers and the Resistance prepare for their next mission. Hiroto and the others have figured out how to open a door located in the lobby of the surface station connected to the orbital elevator, their next objective. They decide to log out for the moment to make further preparations before continuing ahead. The stage for what appears to be their last mission will be outer space.

After a mutually frustrating conversation with the entity that calls itself Alus, the Build Divers temporarily withdraw from the moon. Awaiting them are a tremendous number of One-eyes, which appear to be led by the Gundam Seltsam. Then Hiroto and the others are shocked by another new development.

After a fierce but futile battle, the satellite cannon hidden inside the moon has unleashed a devastating beam. Its effects reach beyond the planet Eldora, extending to all of GBN and even the real world where Hiroto and the others live. It appears that their previous battles may not have been all a game, but actual events instead. Hiroto is completely bewildered by this unimaginable development. But he is no longer alone. It is now inevitable that the Build Divers must meet in real life.

Freddie, an inhabitant of the planet Eldora, sets foot inside a ruined temple, carrying with him a book he accidentally discovered in a storage room. His curiosity leads to an encounter with Hiroto and the other Build Divers, and nobody could imagine what will result from this beginning...

Once again, Hiroto and the Build Divers make contact with Freddie and stand on Eldora's soil. Their sense that the planet Eldora really exists, and isn't just a GBN Story mission, is reinforced. But meanwhile, where their Gunpla are concerned, they must deal with a situation dramatically different from before.

Riding in a balloon made by collecting the lanterns from the Space Crossing festival, Parviz and Freddie go to meet the sacred beast Cuadorn, which dwells in the floating temple known as Milaag Mountain. Buffeted by strong winds, the balloon continues its ascent, but ahead of it lies a huge thundercloud like nothing they've never seen before.

Hiroto and the Build Divers have finally met with the sacred beast Cuadorn, only to be rejected. But after they unflinchingly convey their feelings towards Eldora, Cuadorn opens its silent mouth. As it begins to speak, it tells them of the lightning from the moon that struck Eldora, and of Alus, the one who unleashed it.

Hiroto and the Build Divers have succeeded in turning Milaag Mountain, the home of the sacred beast Cuadorn, into their new base. As they hold a strategy meeting to save the people of Eldora from the One-Eyes, images of Hiroto's own Gunpla and the Alus Earthree Gundam created by Alus are superimposed in Hiroto's complicated thoughts.

Their battle with the Alus Earthree Gundam has ended in victory for Hiroto and the Build Divers. In front of its wreckage are the Earthree Gundam and the Beam Shoot Rifle U7, which has been thrust into the ground. As Hiroto stares at the rifle which looms like a gravestone, a buried memory is revived within the depths of his heart.

Their battle with the Alus Earthree Gundam has ended in victory for Hiroto and the Build Divers. In front of its wreckage are the Earthree Gundam and the Beam Shoot Rifle U7, which has been thrust into the ground. As Hiroto stares at the rifle which looms like a gravestone, a buried memory is revived within the depths of his heart.

Once again, Hiroto and the Build Divers gather in real life. To save the people of Eldora from the One-Eyes, they must power up their Gunpla to resist the powerful new enemies created by Alus, and discuss how to rescue Masaki Shido, whose mind is still trapped on the planet Eldora. Then Parviz makes a surprising proposal.

Thanks to the efforts of Hiroto and the Build Divers, Masaki Shido has been successfully rescued. Hiroto, Kazami, Parviz, and May gather at The Gundam Base to pay a visit to the awakened Masaki. Suddenly, they hear the roar of a motorcycle engine. The rider is someone they never expected.

In preparation for the final battle with Alus, Magee has arranged a rehearsal mission based on the Lotus Challenge, one of the hardest in all of GBN. Hiroto and the Build Divers are the challengers, and awaiting them are a horde of famous and powerful Divers, including the Force members of the original Build Divers.

After successfully completing their rehearsal mission in GBN, Hiroto and the Build Divers gather at Milaag Mountain and prepare for battle. Suddenly, one of the summoning pedestals begins to glow, and another Diver forms from the Eldorium mirror sand.

Alus has chosen to forcibly invade GBN in order to eliminate the people of the Gunpla. But lying in wait for his forces are the Divers of the Coalition of Volunteers, assembled now for the third time. The mission of Hiroto and the Build Divers, which began on the planet Eldora, finally enters its last stage.