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By 2039, blood and DNA tests had become mandatory for several of the "doomsday" viruses or genetic abnormalities that had threatened mankind. When a broad-spectrum immunity factor was discovered in human DNA, the law went one step further. Babies would be engineered with the immunity factor, no exceptions. Automated testing would become routine.

Many - later, most - families opted to go further. If a child could be made resistant to disease, could the genetic engineers go further, making those children smarter, stronger, or better as well? The mechanics of genetics were well understood. Germline engineering became the new normal. A generation of "designer babies" came to dominate the world. George Glenn, astronaut and later the man who will be known as the first "Coordinator", is born in 2039.

In 2039, Shu Ouma is an ordinary high school student in Japan. GHQ has locked the country down. Patrols are everywhere, ready to drag away any Apocalypse infectees. The infection is easy to spot: the virus literally transforms parts of the body into a strange crystal, in reality solidified vril. Shu encounters Inori Yuzuriha, who introduces him to the anti-GHQ resistance cell "Funeral Parlor" and its leader, Gai Tsutsugami.

Through a series of events, Shu obtains the Void Genome - a modification of the Apocalypse Virus capable of extracting solidified vril from a person and transforming it into a tool or weapon appropriate to the donor's personality. These creations of vril are called "Voids". The Void Genome creates a specialized gland in the right arm of the user, and loss of the arm means the user is unable to conjure Voids. In addition, the destruction of a person's Void leads to a fatal and near-instantaneous transfiguration into solidified vril.

With Funeral Parlor's help, Shu fights back against GHQ. The organization responds with even more force, finally partitioning Tokyo completely and isolating all residents. After much struggle, betrayal, and heartache, Shu and his friends manage to purge the Apocalypse Virus itself from Japan. GHQ eventually relents and releases Japan from their control. Shu and his allies retreat into obscurity, but not before confronting Da'ath and their "envoy" Yuu, who have attempted to use the Void Genome to take over the world.

In the next 20 to 30 years, disease is all but eradicated. Society is a fearsome police state, closely scrutinizing people and their health. Any corporation dealing with genetic engineering is strictly monitored, to prevent another apocalyptic virus or biological monstrosity. The high level of tension leads to several wars: the Pan-Asian war, the Third Gulf war, and others. While traditional bioweapons are considered verboten, genetically engineered super-soldiers are created and deployed in these conflicts. During peacetime, society struggles to re-integrate its living weapons.

By 2053, animal-human hybrids and genetically engineered humans are a fact of life. Edward Douglas's report on Dr. Moreau's activities has led to a long-standing fear and mistrust of any such creatures, and half-human "Moreaus" and engineered "frankensteins" are second-class citizens at best. Private detective and tiger-human hybrid Nohar Rajasthan is hired to investigate the death of a conservative anti-moreau politician, which leads him to uncovering evidence of Da'ath. Nohar only learns hints: Da'ath seems interested in pushing humanity away from a mechanistic technology and toward a biotech-driven future, one that they can control with their mastery of biology.

Humanity turns to space to satisfy its need for natural resources, as the exhausted Earth has suffered. Nation struggles against nation, even as the "Cosmic Calendar" is inaugurated in 2055 in an attempt to bring a fragmented world back together. Many older Moreaus are re-activated as soldiers, and second-generation Moreaus are offered full citizenship in exchange for military service in the new conflict.

Artificially created Frankensteins, such as the Nexus-6 Replicants created by the Tyrell Corporation, are extensively used in space, both as workers and soldiers in the ongoing conflicts. Some escape to Earth, only to be hunted by specially trained police units called "Blade Runners". One such group manages to get to Earth, then kill the head of the Tyrell corporation, noted geneticist Eldon Tyrell. Meanwhile, the Rossum Corporation continues to use its "Active" technology in the creation of cloned humanoid automatons called "Universal Robots", who can be mentally programmed for highly skilled and specialized tasks.

Nuclear weapons are deployed on the front lines of central Asia, in the Kashmir region, in 2056. The wholesale destruction of Kashmir's industrial facilities reduces much of the fighting to hand-to-hand or close-quarters combat, where the Moreaus' natural talents give them a decisive edge.

Biological weapons are unleashed around the world as well, killing even civilian populations or threatening them with organ failure. Companies like GeneCo emerge, providing synthetic organs to the sick for a profit. Organ "repo men" exist, who will reclaim such organs - and coincidentally harvest the other organs of a defaulting client who dies during "reclamation" - if the client doesn't keep up their payments.

The formal end of the "Reconstruction War" is in 2064, or C.E. 9 in the new calendar. The construction of the Lunar city, Copernicus, begins the next year, and is completed in 2067 (C.E. 11).

Unlike earlier wars in the century, the Reconstruction War is generally seen as ending well for all involved. The public has been familiar with Moreaus for a generation, and their heroic feats and victories in battle shift attitudes positively toward genetic engineering.

By 2070, designer babies are the default condition for the developed world. The population is divided into "valids" (those with engineered DNA and no handicaps) and "invalids" (those born naturally). The Gattaca Aerospace Corporation begins planning a mission to the Jovian moon of Titan. Vincent Freeman, an "in-valid", has dreamed of space flight since he was a child. He obtains the aid of Jerome Morrow, a "valid" with excellent genetics who was crippled in an accident, to pass himself off as a genetically acceptable "valid".

Vincent is successful in getting aboard the Titan mission, and serves under senior astronaut George Glenn. Scientists studying L. Bob Rife's "metavirus", and the Apocalypse Virus meteor responsible for Lost Christmas, have traced both to the Jovian system. The Gattaca vessel, named "Tsiolkovsky" after the Soviet rocket scientist, will spend seven years exploring Jupiter. Their hope is to establish whether or not extraterrestrial life - even a virus - really exists.

Before leaving, Glenn makes an impassioned speech to the world's population, asking that genetically engineered people become "Coordinators" rather than controllers, guiding mankind rather than ruling it, and urging a more egalitarian society. Unfortunately, his message is not received as intended, and societal friction arises between the "valid" and "in-valid" factions. "In-valids" claim a new name for themselves: "Naturals". In 2072, the bioterrorist group Blue Cosmos launches attacks against hospitals performing genetic enhancement on unborn children.

In 2084, the Tsiolkovsky returns from Jupiter with "Evidence 01", the first known extraterrestrial fossil.

The first permanent L5 space colonies, called PLANTs and shaped like extended hourglasses, become ready for population. Due to the demands of living in space full-time, only Coordinators - now the accepted term for all genetically-engineered humans - are accepted aboard. The PLANTs become a nexus for scientific progress and artistic accomplishment due to the presence of so many "improved" humans. The next year, anti-Coordinator terrorism is aimed at PLANT inhabitants who come to Earth, driving a wedge between the space-dwelling Coordinators and the planet-bound Naturals.

On February 5 of C.E. 70 (2125 AD), a joint peace conference being held at the lunar city Copernicus is struck by a terrorist attack, wiping out the entire United Nations's leadership. War breaks out between Earth and the Plants on February 11.

The Treaty of Junius in C.E. 73 marks the end of hostilities, but fails all of its major political objectives. A second war soon breaks out, which includes nuclear strikes and other weapons from both sides. After much heartbreak and sacrifice, including the deaths of senior leaders on both sides, a ceasefire is announced in C.E. 74.

Blue Cosmos releases a final apocalyptic bioweapon attack that spreads across the world, but ironically fails to contaminate the PLANT population. Earth's remaining human population is nearly obliterated as a result. Lacus Clyne, then leader of the PLANTs, announces that a plan to reboot the devastated Earth's biosphere. Corrupted soil must be purified; radiation must be purged. The effort will take centuries. In the meantime, many Coordinators leave Earth orbit, in an effort to colonize the Jovian system.

The PLANT repopulation plan involved the creation of a vast forest (to leech poison from the soil) and the engineering of giant insect guardians (to reboot the animal-plant biosphere). The Alliance-PLANT wars are remembered a millennium later as "the Seven Days of Fire" by human survivors on Earth, and the forest becomes known as the "Sea of Corruption" for the poisonous miasma found there. The human population has formed kingdoms such as Torumekia and the Dorok Empire, echoing the return to Medieval form once seen in Scotland during the Reaper outbreak. Such kingdoms live in uneasy alliances with each other, as well as struggling to survive the spreading Sea of Corruption itself.

During this time, Nausicaa, princess of the Valley of Wind and daughter of its king Jhil, forms a strange bond with the insect life. She functions as both scientist and mediator, studying the forest and searching for ways for humans and the forest to co-exist. During this time, she encounters Princess Kushana of Torumekia, Asbel of Pejite, and other national leaders, and tries to convince them - with varying levels of success - that cooperation is better than war for ensuring human survival. She penetrates to the heart of the forest, learning of the ancient humans' plan to reboot the Earth at the cost of the lives of those now on the planet.

Faced with the choice of allowing ancient humanity to return to the planet of their birth, or saving the lives of those now living there, Nausicaa disables the computer which manages the reclamation program and would have otherwise sent a signal into space when the plan was complete. The Sea of Corruption will continue to spread, eventually unifying into a single functional entity.

Human beings are now forced to live within the forest, adapting to it and adapting it in turn to their own needs. In effect, humanity is now a virus with the world as its host. Only time will tell if its presence is beneficial or not.