The time is the year 2031 and humans have been replaced by the Blue. Yuji Kaido awakens to this world after 22 years and his only hope to stay alive is the Sleeper Recovery Team.
Yuji learns the truth about the Blue and the nightmare the world has become while he slept.
Tired of feeling like a man without purpose Yuji demands to be taught how to fight.
Yuji breaks orders from Marlene to save a little girl whom he promises to protect. He follows her back to her home and finds more survivors of the Blue.
The team must contact Second Earth and with the Blue moving in on their position. Only one choice is left and that is to use the humans as a diversion.
Yuji and Marlene head toward the space station but along the way their tempers start to flare.
Yuji and Marlene meet Dice while still struggling to reach the space station. A rough and tumble ex-soldier who gave up the futility of fighting the Blue.
Yuji is separated from Dice and Marlene during a sandstorm. He is rescued by a group of Nomads and begins to think a normal life may be possible.
Marlene, Dice, and Yuji are reunited at the nomad camp. Marlene wants Yuji to continue the quest for Second Earth but he refuses.
Finally after much adversity Marlene and Yuji reach the space station and find they're not alone. Other soldiers are also looking for a way to Second Earth.
Just as it appears that the launch will finally happen without further problems A mad soldier high-jacks the escape ship in an attempt to kidnap a woman he's obsessed with.
Yuji is rushed to intensive care after the surprise attack of a sleeping blue aboard the shuttle.
When Yuji disappears from his quarters Marlene takes it upon herself to find him. With the station on full alert Marlene must find the man who'll most likely know where Yuji is hiding.
After a failed attempt to free Yuji from the laboratory he's being held in. Marlene must once again face an inquiry into her actions but this time she has Yuji by her side.
Yuji is put into an intensive combat training program and meets his squad-mates. Members of the newly formed sleeper brigade.
A large attack force is sent to the Earth as the first wave in an attempt to retake the planet from the Blue. During the attack Yuji is left in shock after Tony destroys a Blue nest by himself.
Yuji's behavior becomes more disturbing as he descends into a cold blooded killing machine.
Seno tells Marlene the truth about Yuji's behavior and the hyperactive Blue cells that are invading his brain.
The Sleeper Brigade launches another attack against the Blue and Yuji continues his descent into insanity.
As the second Sleeper attack continues to fail Marlene rushes headlong into the fight.
Marlene and Yuji head back to Second Earth with Tony in the full grip of the Blue cells.
Yuji and Marlene gain entry to the now Blue infested station with their objective to kill Tony.
After beating impossible odds Marlene and Yuji make it to the control room. Now with Tony standing in their path they face their hardest fight yet.
As the survivors of Second Earth try to rebuild after Tony's attack Seno makes plans for a new way of life.
Satellite photos show a massive move of the Blue in South America but upon landing on Earth it becomes clear that the Blue have actually disappeared.
Yuji prepares to fight the last Blue and find the answers to all that has happened.