In Act 1, Nagisa and Iczer-One meet when the Cthuwulf attack. The aliens send their biomechanical Voids and trap Icezer-One and Nagisa in dimension subspace. Later, Commander Cobalt launches an attack against Magisa's city using the Dilos-Theta mecha. Iczer-One must convince Nagisa to join her and challenge Cobalt with their mecha, Iczer-Robo!

In Act 2, a Cthuwulf fortress arrives on Earth. Nagisa begriends a young girl while Iczer-One investigates the alien fortress. Iczer-One becomes trapped in subspace and Nagisa is forced to protect the young girl from the parasitic monsters. Iczer-One escapes only to face the challenge of a new enemy, her "sister" Iczer-Two!

In Act 3, Nagisa and Iczer-One battle against Iczer-Two's mecha, Iczer-Sigma. Later, the leader og the Cthuwulf, Big Gold, orders Nagisa's capture and conversion into Iczer-Two's partner. Iczer-One must try to save Nagisa and defeat her sister and Big Gold in a final battle for humanity's survival!