Aoba Watase is a normal first year high school student coming back to school after summer break when a mysterious robot comes after him. He has never seen it before, but its pilot seems to know him and wants him dead.

One minute, Hina is disappearing, telling Aoba that Dio is waiting for him. In the next minute, Aoba finds himself in a strange cockpit alone, thrust into the middle of a furious firefight.

As Aoba tries to come to grips with this new world that he's found himself in, the ship he is on comes under attack again. And during this engagement, he unexpectedly comes across someone he knows.

Aoba faces the consequences of his rash actions during combat when he saw Hina. And later, the Cygnus lands at Narashino and Aoba gets a chance to explore his hometown to see what has become of it in the last 70 years.

Aoba finds out more about Dio and his family. And later, Cygnus unexpectedly finds itself being mobilized against an invading Zogilian force.

After being mobilized, the Cygnus and the Coupling Valiancers are no longer a secret. In order to defend their existence against outraged politicians, a film crew arrives to make a promotional video to rally popular support.

As the Cygnus makes its way to the Hawaii Base, Zogilia's Protection Division catches up with them. And the three Coupler pilots must decide who will pair up with whom.

Aoba finally gets some time to talk to Hina, but as they try to survive the night on the island they crash-landed on, he has a frustrating time trying to get through to her.

Discouraged by his encounter with Hina, Aoba mopes around, but Dio finds his sniveling, defeatist attitude unacceptable, especially once they come under attack yet again.

The Zogilians infiltrate the Hawaii Base. While the crew of the Cygnus work to thwart them, Hina's father reveals a startling truth to her.

The crew of the Cygnus work through the fallout of losing the Luxon and the Bradyon, and of the flawed Coupling that Aoba and Dio conducted using the old Coupling Valiancers.

With over half their fleet gone and up against enemy Coupling Valiancers, the Cygnus is tasked with taking down the Gorgon, Zogilia's weapon of mass destruction.