As the virus outbreak grows out of control, Yuuji slowly recovers from his injuries from before. In the face of growing danger, Yuuji begins to realise how much Ai means to him. Yuuji races to the aid of Ai as he leads the remaining armed forces against the new mutations.

The NOA soldiers return to the home base to begin what they think is a break from the action. One by one, they begin to show symptoms of being infected, except for Yuuji. A new strain of the M34 begins to emerge, bringing the NOA soldiers face-to-face with this new unstoppable threat.

Yuuji is hospitalised due to injuries from the last battle as the rest of the NOA team heads off into the battle. In the heat of the battle, Ai discovers the horror of the M34 virus as Yuuji confronts her fears and his own insecurities.

In a world under attack by the rampant M34 virus, the NOA soldiers stand as the best line of defense against the new strains that keep emerging. One soldier, Yuuji, is torn between duty and his place in the world until a chance meeting with a shy girl named Ai, the agency's latest weapon and mankind's newest hope.