In an attempt to rid the planet of 'Shadow Zone' (slum areas), the government of Taowajan continues its campaign of 'urban renewal.' Unwilling to put up with the constant struggle to survive, Komimasa and Kei decide to stow away on the next available ship to Myce. Unbeknownst to the two young travellers, the ship's primary passenger happens to be Dr. Touka, the foremost expert on Zeiram, who is on his way to Myce to investigate reported sightings of Zeiram on the planet. And to make things even worse, the ship become the target of some very desparate hijackers... Iria, having just received her accreditation, lands her first job as a full-fledged bounty hunter.

Iria visits her home province of Batabitajira, only to be attacked by a Zeiram-produced clone. Yet Iria senses that somehow, this encounter with the Zeiramoid being was no accident, and somehow, it was waiting for her...

Meanwhile, citizens of the Capital City of Myce are disappearing at an alarming rate. Worse still, it seems that more and more hideous creatures are being unleashed upon the city. And at the epicenter of all the activity stands Zeiram, who can not only produce genetically cloned beings to do his bidding, but also call more Zeirams from beyond the Mycean planetary system...