It is the year 2031. Humankind has been replaced as the dominant species on Earth by a race of monstrous insect-like creatures known as the Blue.
Yuji learns the horrible truth about the Blue. Their infestation of the planet has forced the human race to seek refuge in outer space.
Tired of feeling helpless in this hostile new world, Yuji pleads to be trained as part of the team.
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.
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.
Still en route to Baikonur, Marlene and Yuji cross paths with a rough-mannered stranger named Dice.
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 Dice are reunited with Yuji outside the nomad camp. Marlene presses Yuji to continue the journey to Second Earth, but Yuji refuses.
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.
When Yuji disappears from the Medical Station, Marlene defies orders and decides to find him on her own.
Marlene?s attempt s to free Yuji from the laboratory in which he is being held are thwarted.
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.
Marlene notices that Yuji?s behavior is getting stranger and stranger.
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 second airborne operation meets with disaster when the Blue counterattack outnumbers Second Earth forces five-to-one.
While Marlene flies a distraught Yuji back to Second Earth, Tony uses his Sleeper skills to infiltrate the High Council.
Yuji and Marlene infiltrate the Blue infested Medical Station and are soon reunited with Rick and Soo.
With Rick injured too severely to continue, Marlene and Yuji continue through the Medical Station alone.
The remaining survivors aboard Second Earth begin to rebuild after Tony?s devastating attack.
Satellite images of the Earth reveal a mass Blue migration in South America, and Yuji volunteers to investigate.
A monstrous Blue has emerged in the heart of the South American nest, the only thing standing between Yuji and the answers he so desperately seeks.