A major incident has occurred in the peaceful Sky Land!? The young Princess Elle has been kidnapped by the monsters of Underg Empire! A brave young girl, Sora, follows the princess through a mysterious hole. "TV"? "Cars"? Are those some kind of magic tools!?!? But there's no time to be surprised! She has to get the princess back to the castle...! Flying between two worlds! The adventure with the Pretty Cure begins now! It's hero time!

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.

In the year 2046 humans are moving away from using robots and begin to trust them less and less. In this time life becomes very perilous for the beings known as seconds. The seconds are the most recent line of robots, as far as the public knows. This is the world Detective Ross Sylibus lives in. Detective Sylibus is transferred to Mars by his request after his partner was killed by a robot. As he arrives he falls headfirst into a murder where a country singer on his flight was murdered. He steps off the plane and watches as a scene unfolds and he meets his partner, Armitage a female cop with a major attitude. A rash of murders begins when yet more women are killed. As the investigation is continued a secret is uncovered. There is another line of robots known as Thirds. More and more Thirds turn up missing, as a serial killer who is intent on wiping out all the Thirds runs rampant. Armitage in her quest to put the murderer to justice reveals a secret. She herself is a Third.

Satake Hirofumi is a prisoner on death row for murdering his fiancée. He's also an "Undeadman" who has survived many desperate situations. For this, he has earned the interest of a research institution called "Human Crazy University," which studies real-life miraculous phenomena and the people who become entangled in them. Now a subject of their research, Satake relates to them his memories of his immortal, yet unhappy, life. Why did he kill his fiancée? Soon enough, the truth sheds light on a much bigger conspiracy...