Humankind has been replaced as the dominant species on Earth by a race of monstrous insect-like creatures known as the Blue. Sleeper Yuji Kaido finds himself thrust into this nightmarish world, suddenly awakened after 22 years in suspended animation.
Yuji learns the horrible truth about the Blue. Marlene and the Sleeper Recovery Team have been given orders to get Yuji to space station Second Earth alive.
Yuji disobeys Marlene's orders by saving a little girl's life, and discovers a group of survivors hidden among the ruins of the city. Yuji makes a promise to the little girl, Yung, that he will protect her from the Blue.
The surviving members of the Sleeper Recovery Team must enter an abandoned communications tower that is now a Blue nest in a desperate attempt to contact Second Earth.
Marlene and Yuji now travel on foot towards Baikonur Space Base. The tensions between the two come to a head, as Yuji confronts the demons that now haunt him in this nightmarish new world.
Yuji is separated from Marlene and Dice amidst the confusion of a sandstorm. He is rescued from the desert by a band of nomads, and is befriended by Elena, a young nomad girl.
Marlene and Yuji arrive at Baikonur, only to find the space base in a state of chaos. The facility is crawling with Blue, and the computer defense systems have turned on their human counterparts.
The lives of the remaining recovery squad members are thrown into jeopardy when a renegade officer attempts to hijack the shuttle and escape on his own.
Yuji is rushed to intensive care after being attacked by a Blue aboard the shuttle to Second Earth. Now, Marlene must face an inquiry before the High Council and defend her recent actions on the planet's surface.
Marlene's attempts to free Yuji from the laboratory in which he is being held are thwarted. Now she must once again stand before the High Council to defend her actions, this time with Yuji at her side.
After beginning an intensive combat training program with the newly formed Sleeper Brigade, Yuji finds himself the object of another young Sleeper's attention.
A large attack force is sent to Earth, the first wave in a new campaign to reclaim the planet from the Blue. Yuji is awed when a fellow Sleeper, Tony, wipes out an entire Blue nest on his own.
Marlene notices that Yuji's behavior is getting stranger and stranger. On the battlefield he is a force to be reckoned with, but he has an unhealthy obsession with destroying the Blue.
Director Miyagi reveals to Marlene the true cause of Yuji's accelerated rate of achievement - an infestation of "B cells" that have begun to eat away at his mind.
The Sleeper Brigades launch yet another offensive against the Blue, and Yuji's lust for battle grows out of control as his B cells begin to take hold of his sanity.
The remaining survivors aboard Second Earth begin to rebuild after Tony's devastating attack. Director Miyagi lays out his plan to make Second Earth the permanent home of the human race.