BioMega follows a character by the name of Kanoe Zouichi and the mysterious Kanoe Fuyu whose luminous form is integrated into the system of his bike. They are agents sent by a powerful organization to retrieve the human with the ability to resist and transmute the NS5 infection that is spreading across the world, named Yion/Ion Green.

However, their mission is delayed by the reckless actions of the Public Health Department's taskforce and the kidnapping of Yion/Ion Green. Will they complete their mission? Where has Yion/Ion Green been taken?