The mysterious life-form Zovaras is deeply connected to both Omega's past and Valgeness, the Meteokaiju who possesses a black Meteo. Zovaras also has a powerful ability to control other kaiju. To save Valgeness, Sorato and Kosei team up with Ayumu and Sayuki. The four of them launch a desperate mission to stop Zovaras, who wants to destroy Omega and conquer Earth—and they even bring the NDF into the fight.

Using a new weapon developed by the NDF, humanity achieves its first solo victory against a kaiju! However, the kaiju, which was clearly defeated and dead, suddenly reanimates! The KSCT and the NDF coordinate a defense strategy, but the situation rapidly worsens. To discover the weakness of this "immortal" kaiju, Sorato and Sayuki fly to the permafrost of the North!