Kim is living a peaceful life with his father as a farmer on their planet until one day when a runaway spaceship is detected moving at a high speed towards his father's farm. To rescue his father Kim jumps on board the ship and manages to land it safely before it crashes. On board the ship he finds a severely Injured lone survivor whom with his dying words begs Kim to take something of his to the Galactic Fleet. He then transfers something that was attached to his arm onto Kim's arm. The thing was a Lens and its transferring should have been impossible and having it has turned Kim into a Lensman. Other than giving Kim unknown powers it also contains vital information for the victory of the Galactic Fleet over the evil Boskone Empire. Kim must now using the spaceship Britannia bring the Lense to the Galactic Fleet. But this is not an easy task when Lord Helmet of the Boskone Empire is willing to use everything in his power to stop him.

Hundreds of years after the 20th century, nature and the ecosystem have been devastated due to use of nuclear and biological weapons. Most of the Earth has been contaminated and is collapsing into ruin, and a great majority of plants and animals are now extinct. The world heads to the "Big Six," the sixth mass extinction event. Humanity built cities in the sky, migrating the endangered species of animals and plants there. Over many years, the animals evolved in these isolated cities. With artificial genetic crossbreeding, they acquire language, bipedality, and build a life and civilization for themselves free from want. No one thinks of the world below any longer. One day, a single plant seed wanders into one of the sky cities, and the children Kui, Hiruma, and Root discover it. Unable to resist the temptation to look into the world outside, they decide to undertake an adventure to the outside world, unknowing that once they set foot on the ground, they will never be able to return.

Due to the incredible success of the Sibyl System, Japan has begun exporting the technology to other countries with the hope that it will one day be used all around the world. In order to test its effectiveness in a foreign location, the war-torn state of the South East Asian Union (SEAUn) decides to implement the system, hoping to bring peace and stability to the town of Shambala Float and keep the population in check.

However, a group of anti-Sibyl terrorists arrive in Japan, and the Ministry of Welfare's Public Safety Bureau discovers significant evidence that the invaders are being aided by Shinya Kougami, a former Enforcer who went rogue. Because of their past relationship, Akane Tsunemori is sent to SEAUn to bring him back, but with their last meeting years in the past, their reunion might not go quite as planned.

One day, when Remu Mikage is on a video call with his sister, Shiki, who has traveled to the futuristic Okinotori-island Mega Float City for school, she confesses that both the audio and visuals of her are completely artificial. In order to be more efficient in her studies, Shiki has used neural-linked nanomachines to upload her consciousness onto a computer and is storing her physical body in a "body pool." While shocked, Remu is supportive of his sister's decision, until the disaster known as the "Early Rapture" happens. The Early Rapture causes everyone who has uploaded their consciousnesses to either fall into a coma or perish. Remu visits his sister's empty apartment one last time, but is shocked when Shiki arrives at the door. With no memory of her family or past, and being pursued by a violent group of researchers, Shiki and her brother are forced to flee using her newfound power of nanomachine manipulation.