When high-school freshman Yomogi Asanaka stumbles across kaiju user Gauma, he and a few unsuspecting onlookers get caught up in a fight against kaiju.

Yomogi and Yume visit the city where they fought the Kaiju and witness the tragedy. He and the others start their Dynazenon maneuver training, but a Kaiju appears again without any delay.

One of the Kaiju Eugenicists, Juuga, tells Yomogi that they were betrayed by Gauma. Yomogi and the others become distrustful of Gauma but they end up having to fight a Kaiju with their hearts in disarray. With their hearts separated, Dynazenon is unable to unleash its full power.

Yomogi catches a cold and goes to sleep. Gauma gets Yume to visit him. Yomogi is confused by Yume's sudden visit, but the relationship between the two slightly unravels. When Yume hears that a monster had appeared, she leaves Yomogi with his cold and heads for battle.

At Chise's suggestion, Yomogi and his friends go to a large outdoor pool, but there is unexpected company there. Gauma orders Yomogi and Yumemi to pretend to be lovers for a certain mission.

Yume hears a rumor about Kano's death from an alumni of the chorus club which Kano was in while she was alive. Meanwhile, Koyomi awakens from a hangover and finds that he has lost Dynastriker. Gauma scolds Koyomi and he is reminded of someone he met the previous night.

Dynazenon is defeated by the Kaiju. A mysterious giant that appears. Despite the confusion, Onija and Mujina begin to fight the giant. Gauma has no way to repair the damaged Dynazenon.

Yomogi and Yume hear about how Kano died. A Kaiju suddenly appears without them being able to take in the story. Meanwhile, Chise holds onto a secret.

An unprecedentedly great power attack the city. Yomogi takes hold of Dynasoldier to confront the root of it all.

Yomogi and the others begin to resume their everyday life, and the Kaiju Eugenicists who have lost their Kaiju also lose their place in the world.

Yomogi and the others combine into Dynazenon once more for the final battle.