Plot
In 2009, Yuji Kaido is diagnosed with a severe illness and is put into cryogenic sleep until a cure is found. In 2031, he is awakened amid a raging war between armored soldiers and insectoid beings called the "Blue", which kill and harvest humans for food. The Blue have overrun the Earth and wiped out most of the human race.
The soldiers are from an orbiting space colony collectively called Second Earth and have been ordered to recover "sleepers" such as Yuji around the Earth. They are led by Marlene Angel, who at first appears to be heartless toward others. On the journey to Second Earth, Yuji meets many of the humans who were left behind during the evacuation due to limited resources. Standing orders for Marlene and her platoon are to consider any human survivors on the surface to be already dead, which greatly troubles Yuji.
On their journey, all of the soldiers are killed except for Marlene, causing Yuji to fall into deep depression as he recognizes the destruction around him and his inability to save those he cares about, especially after failing to save human survivors from a swarm of Blue in Seoul. During their travel to the Baikonur Cosmodrome through the mountains of Central Asia, Yuji and Marlene develop a bond that softens her sharp edges and they become romantically involved with one another. Upon reaching Baikonur, Yuji and Marlene encounter another group of soldiers and after fighting off more Blue, they escape on the shuttle. During the flight to Second Earth, a mutated Blue hidden in the shuttle attacks Yuji, critically injuring him.
Yuji and Marlene are separated upon arriving at Second Earth, and the High Council demotes Marlene and sends her back into training at the education station as punishment for failing to protect Yuji. Not knowing what happened after he was attacked, Marlene rebels and is determined to find Yuji. When she does, she finds he has healed and is being trained to use a new specialized sleeper-specific mech called the Double Edge, which is much stronger than the originals used in the war against the Blue. It is revealed that Yuji's illness is the key to destroying the Blue and taking back the planet. Yuji and the other Sleepers have B-cells, which are also the genetic makeup of the Blue.
The High Council reluctantly agrees to reinstate Marlene and allow her to work with Yuji again. After intensive training, they return to Earth with two other Sleepers - Tony Frost and Alicia Whistle. They and the other forces of Second Earth battle the Blue, successfully destroying the most enormous nests across Africa. However, the battles begin to harm Yuji, who has minimal regard for human life and is utterly obsessed with surpassing Tony in killing the Blue. Yuji's actions deeply concern Marlene, and she begins to realize something is wrong.
Shortly after returning to Second Earth, the High Council orders the Sleepers on a second offensive against the Blue in New York City. As the Sleepers are carrying out their mission, a battle on Second Earth between two factions is waged. Seno Miyagi, the director of Second Earth's science division, leads the Ark rebellion and seizes control of the military, lunar resources, and education stations of Second Earth from the High Council, who escape to and retain control of the medical station. Seno reveals to Marlene the nature of the illness that put Yuji in stasis, the source of his abilities, and the source of the Blue: they are a defense mechanism enacted by the Earth to purge the existence of humanity, and the B-cells that exist in the Sleepers could become a potential threat to humanity as well.
After the Ark successfully takes over Second Earth from the High Council, Marlene heads down to New York in search of Yuji. When she finds him, his B-cells are beginning to activate, and goes berserk as a killing machine. After struggling with him, Marlene is finally able to get through to Yuji and helps him overcome his madness by showing him her human emotions and feelings. Meanwhile, Tony and Alicia abandon the remaining ground forces as their B-cells have fully awakened. They return to Second Earth with several Blue when they board the medical station, killing most of Second Earth’s high command.
Tony and Alicia plan to ram the medical station into the military station to destroy Second Earth. They see this as the "Grand Will of the Earth", in which they will become "messiahs" and cleanse Earth of humanity forever. Yuji, Marlene, and a group of other soldiers infiltrate the station and subdue Alicia. Yuji then confronts and shoots Tony. Alicia ventures back to Tony to die with him as the military destroys the medical station.
Seno's junta decides to abandon Earth, and Yuji becomes depressed and contemplates his existence, wondering what he has been fighting for, why he was awakened, why he cannot save his friends, and what Earth's true will is. However, Marlene manages to reconnect with Yuji again; they agree to convince Seno to let them go back to Earth and fight the Blue, and finally become lovers.
After discovering a new migration pattern of the Blue, Seno agrees to let Yuji and Marlene lead a group of volunteers to an area in South America where a massive nest is located. The nest seems impenetrable at first, but they eventually find an entrance with the help of the local people. The entrance leads to a tunnel where the walls, ceiling, and floor of the cavern are composed of fossil-like Blue. The team finally comes upon a crystal formation in a massive cavern. A huge Blue is born from the gel substance sitting atop the formation and kills everyone except for Yuji and Marlene. Yuji kills it and concludes that the sphere will hold the answers he seeks. He sends Marlene, who is pregnant with their child, to the surface to regroup with the remaining volunteers and wait for him. He then gets a vision and can see what the Earth itself can see. Yuji comes to understand how mankind can live alongside the B-cells and returns to Marlene.
Meanwhile, Second Earth's citizens revolt against Seno and kill him, and then begin abandoning the station for Earth via shuttles. A firefight erupts over the last remaining overcrowded shuttle, and a massive explosion destroys the station. All around the world, from former Blue Nests, long strings of coalescing energy ascend into Earth's atmosphere and form a ring. Yuji and Marlene watch this, realizing Earth is now safe again, and look forward to the rest of their lives together as the sun sets.
