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.

Rikotto, Zuzu, and Paroru are intelligent furry creatures who believe more than anything that the world outside their island is too dangerous to explore. Despite this, Rikotto and Zuzu long to see the world that produces the mysterious objects that wash up on their shores. After a particularly exciting find, Rikotto convinces Zuzu to build a boat, and they set sail across the sea with their reluctant friend Paroru in tow. At first, the trio finds the foreign land beautiful and exciting, but they are overwhelmed when they come across a bustling city of humans. When Rikotto and Zuzu get captured by a circus ringleader who intends to put them on display, Paroru has to decide what fears he is willing to face for his friends.

Legend says that centuries ago, a colossal spider ravaged Tokyo. Resistance was futile, as none could quell the havoc wrought upon the city by the beast. Fortunately, one man—the legendary exorcist—stopped the devastation. Using his divine powers, he sealed the monster away and the world has enjoyed peace ever since. Mizuki Henmi is an adolescent girl who is acquainted with Shu Suzuri, a dull young man who runs an old Japanese bookstore. During a routine visit to his store, Mizuki learns of a mysterious and valuable book that Shu is planning to sell. Unfortunately, the unrestrained Mizuki handles the book roughly, breaking the seal that kept it shut and revealing an odd entity—a cute spider. Wasurenagumo tells the story of Mizuki, Shu, and their seemingly harmless spider. However, ominous winds begin blowing. While Shu is infatued with his arachnid friend, Mizuki becomes wary of its every move…

A young girl named Tomoko visits the Hiroshima Peace Memorial. There she has a mysterious meeting with Sadako, the little girl who was 2 years old when the U.S. dropped the bomb on her city during WWII and 11 when she died from the effects of radiation poisoning. Sadako takes Tomoko on an eye-opening journey.