In 2100, the newly built Bayside City serves as Japan's premier international port. The Angel Arms Company is established by a former policewoman named Takako, to help wage war on terrorism with armed security suits. When the mayor is assassinated, the women of Angel Arms end up protecting the evil crime-lord Hassan, in hopes that his information will help bring down a global terror ring. Takako's back is to the wall as a band of criminals plot to kill Hassan, and the organization's leader is revealed to be the former lover of Angel Arms' own Alisa.

Strange events begin to occur as a withdrawn girl named Lain becomes obsessed with interconnected virtual realm of "The Wired".