Yukina, a sophomore at Tateyama High, visits Kurobe Laboratory when it is suddenly attacked. While escaping, she touches a mysterious cube.
Kennosuke Tokisada Ouma appears from the cube. He tries to save Yukina but is knocked unconscious. A new large scale geoframe emerges from Toyama Bay.
Kennosuke, with Yukina along for the ride, is victorious, but the enemy geoframe gets away. He is captured once again but escapes and finds Koharu.
After realizing the extent of his slumber, Kennosuke is invited by Yukina's uncle to live with the family. The modern world continues to confound him.
Yukina returns to school, hoping life is finally going back to normal -- only to be horrified when she catches a glimpse of the new transfer student.
Ken and Yukina resume their battle with the Yellow Crab mecha. Classmates Akagi and Kayahara defy the authorities and head closer to the battle zone.
After the Yellow Crab's pilot takes his own life, Yukina loses her will to fight. At school, she hears that Akagi and Kayahara are still missing.
As the invaders’ demands cause friction, Yukina leaves home to avoid battle. Kennosuke goes to search for her but realizes he knows nothing about her.
An enormous enemy geoframe appears, but with Yukina missing, the center lacks the power to oppose it. Ken, Akagi and Kayahara continue the search.
The captured pilot is taken back to the research center and questioned. He says that he came to find a certain object. Ken appears to recognize him.
The enemy pilot unexpectedly escapes and is able to restore his geoframe. Yukina is ordered to deploy in the Kuromukuro, but runs into him on the way.
Summer vacation has come, and that means more training for Ken and Yukina, who is improving more than she expected. Akagi hopes to become a pilot.
Ken's Kuromukuro fights alongside the GAUS to drive off a giant geoframe. Meanwhile, Kayahara's plan for the Culture Fair stirs up excitement.
Kennosuke has been run through by a woman with the face of his princess. Before she can finish him off, a mysterious figure leaps to his defense.
The local population begins to evacuate the area, and the school's students are transferring out. Carlos doesn't know what to say about his situation.
Sophie shows excellent results in the single-pilot GAUS, impressing Ken. Soon, he learns that her parents expect her to leave Japan.
Graham orders a comprehensive search to find the two missing enemy pilots. Meanwhile, the Efidolg mothership dispatches an additional geoframe.
Yukina and a reluctant Ken receive their salaries and decide to go to the hot springs together. Rumors of their plans spread through the school.
The Research Institute panics over Yukina's disappearance. Dr. Hausen makes a surprising discovery. Meanwhile, Sophie receives a mysterious message.
Ken is on the way, but Yukina is already planning her escape. She encounters Mirasa, who attacks. Meanwhile, Sophie learns more about the enemy.
Ken and Yukina have safely returned but have no time to celebrate after the research center learns that the enemy mothership will soon land on Earth.
The enemy blockades the research center. At home, Yukina and the others are educated about the Efidolg and Yukina's missing father, Takehito.
Ken and Yukina take Muetta to school, causing a stir among the few remaining students. Carlos announces the completion of his movie scenario.
Seeking the truth, Muetta turns against her former comrades. Realizing that the deciding battle is approaching, everyone makes their preparations.
Ken and Zell are shocked to learn of a power that can resist the enemy. Everyone at school is tired of waiting for Yukina and the others' return.
Through the fight with the Efidolg, the characters find themselves closer to their aims. Kennosuke discovers the path he must walk.