In 1990, aliens invaded Earth, but after 40 years, through the combination of nuclear weapons, technological ingenuity, and human grit, the aliens were repelled.

Now, 2045, aliens are choosing the discreet approach to quietly invade Earth’s surface and cause disruption from within human civilization. Many nations have created secret agencies highly trained in counter-extraterrestrialism warfare, tasked with taking out aliens in the shadows without alerting the public.

In Japan, the National Diet created the counter-extraterrestrialism agency, “the Bureau of Extraterrestrial Riddance,” or simply “the BXR.”

In Shinjuku Ward, a strange quantum reading was detected in a closed-off section of the Shinjuku Subnade, Shinjuku’s largest underground shopping mall in Kabukicho.

Agent “Mori Jubei” is sent to handle the threat. With the aide of the ATLAS and an arsenal of weapons, he goes alien hunting.