MUSICAL BIOHAZARD ~ Voice of Gaia ~ is set in an unspecified year where the threat of bioterrorism has continued to increase in extremity. Much of the story is set in and around the walled Croatian city of Dubrovnik, on the Adriatic seacoast, which faces attack from "Them", zombies infected by an ancient virus. The survivors in Dubrovnik are protected by both their wall and by music, as melodies are known to calm Them, surprising their violent urges.

Train otaku Shinpei, his two geeky friends, three jocks, and the school “princess” Tsubaki are trapped in a school together as police, led by Tsubaki’s dad, mistake the boys for kidnappers. Meanwhile, the true culprit orchestrates this tense situation from afar.