Iria, the young assistant bounty-hunter for her brother, Gren, is illegally out on her own job, only to have the bounty stolen from under her by a competitor, Fujikuro. Aware that she's unable to do anything legally, Iria has no choice but to let Fujikuro take her prize... Meanwhile, Gren has been given a choice assignment on behalf of the Tedan Tippedai Corporation: the rescue of the passengers and cargo of their starship, Karma, which has been hijacked by an unknown assailant. But there's a catch: the rescue must be carried out before the authorities arrive.

The destruction of the Karma forces Iria to crash-land on the resort planet of Taowajan, uncertain of both Gren's and Bob's fates. Iria discovers that even in remote areas of the Galaxy, bureacracy reigns supreme. She's unable to book free passage back home, leaving her stranded on a wannabe resort area. But the same forces which caused her to land on Taowajan has also produced a most unwelcome visitor: Zeiram! Unwelcome, that is, for all but the planet's administrators. Overrun with a poverty-level population, the government decides to let Zeiram run amuck, carrying out an informal "urban renewal" project. Now it's up to Iria and her new-found friends to make sure that this doesn't happen. And she might just be able to pull it off, with the help of her brother Gren.

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...

Severely injured during her last battle with Zeiram, Iria finds herself more reluctant to go after Zeiram -- at least not without some advantage she might be able to use. But Kei is not so cautious. Frustrated by Iria's apparent lack of initiative, Kei decides to go after Zeiram herself, only to be stopped by Fujikuro.

Meanwhile, the Mycean council's plan to build a huge transemmbler is met with forceful opposition by the Zeiramoid clones. Zeiram has resisted every know weapon on the planet, and the only plausible solution seems to be to transport it off world, and make it someone else's problem. But Iria knows the only solution is to stop Zeiram permenantly...