The game takes place in an alternate history in 1906 where the British Empire rules all of Earth and several extrasolar colony worlds, powered by technology brought to the planet by Halley's Comet in 1835. An unknown substance known as Halley's Core was found throughout the world, and certain individuals who came in contact with it and gained superhuman abilities became known as "Halley's Chosen." The first of these was a scientist named Dr. Hebble Gate, who was affected by the comet while in his mother's womb. With his superhuman mind he harnessed the power of Halley's Core and discovered a wide range of scientific breakthroughs, including fusion and nuclear power, genetic engineering, computers, space travel and countless others. With these technologies the British Empire quickly conquered the earth, and Gate is famous as the man responsible. A complete mystery to all, Gate also holds great power over economic, political and military affairs, and is the founder of the Hebble Foundation and the GunValkyrie (GV) Organization, composed of Halley's Chosen throughout the world to prevent the misuse of technology. He suddenly disappears, throwing the world into shock, and has been missing for four years by the time the game begins.
In addition to his disappearance, the residents of the colonized planet of Tir na Nog have also disappeared, with an outbreak of large alien creatures that resemble giant insects in their place. It is also believed that before his disappearance, Gate was conducting research on how to strengthen the colonists through genetic modification, and it is speculated that the insects and colonists are one and the same.
In response, members of an elite military force within the GV organization, known as "Team Dolphin" (established 1887) is sent to investigate Gate's disappearance as well as the situation on Tir na Nog. Leading the investigation is Gate's only daughter, Lieutenant Meridian Poe, who survives on a life support system developed by her father after he surgically removed her head and disappeared with her body. The two playable characters are Kelly O'Lenmey, born in Ballymun, Ireland, a collected idealist who once aided the Irish Republic in their fight for independence until their methods caused her to leave and join the GV, and Saburouta Mishima, born in Kyushu, Japan, an exiled Samurai of the Meiji Restoration who was saved by the GV after he was unjustly sentenced to capital punishment.
Dr. Gate's fate at the end of the game left ambiguous, as the Poe's Report documents presented throughout the game reveal that a body was eventually discovered, but its identity is not confirmed.