When Yun Arikawa and his partner, Haberu Katou, investigate a house rumored to be haunted, the last thing they expect is to stumble into a mystery that will soon envelop the entire planet. While measuring strange radio signals, they receive a call from Mei Kamino, a graduate student investigating the same signal and using the equipment their company previously installed. After an odd night, Yun returns to work at Ootaki Factory, a tech company that actually exists to produce Jet Jaguar—a robot that conspiracy theorist Gorou Ootaki has dreamed of creating. However, when flying dinosaur-like creatures known as Rodan are attracted to the strange radio signals, Jet Jaguar seems to be the only force capable of fighting them. As Yun and Mei investigate the Rodans' sudden appearance, more dangerous monsters begin to surface from the ocean—along with enigmatic red dust.

Despite endless research, the human mind remains a mystery to this day. Unknown to the public, there exist special individuals who are able to dive deep into the minds of people and even manipulate their memories. Gifted with this ability, Hiroki, Tsukasa, and Satoru are among those who use their power to commit crime under the orders of their leader, Katsuragi. The three step into the dangerous territory of the human mind in order to destroy their assigned targets while striving to keep their own minds and memories safe.

Koyomi Araragi spent his last year of high school helping girls in his town resolve various supernatural afflictions. But now Araragi has departed for university, leaving his friends to fend for themselves against new problems and curses that plague them. Yotsugi Ononoki, once a human corpse and now a living doll, takes residence in Araragi's home, keeping watch over his sister Tsukihi, a girl harboring a mystical secret of her own. As part of her duties, Yotsugi fills Araragi's vacated role as occult expert, assisting others in town with their issues. One of these girls, middle school student Nadeko Sengoku, slowly recovers from her own recent brushes with the paranormal. She avoids returning to school, instead spending time alone in her room and pursuing her dream of becoming a professional manga artist. In order to speed up Nadeko's quest for mastery of her craft, Yotsugi convinces her to create four copies of herself, each representing a distinct aspect of Nadeko's personality. However, the clones refuse to help Nadeko, instead escaping into the town and creating a chaotic mess. Now forced to grapple with her own fractured sense of identity, Nadeko sets out to capture them and resolve her inner conflict.

Life seems to drift by for Kana Koumoto and her friends in their small Japanese town. Every day is just like the last, and it feels like every new day will be the same. Kana goes to school, hangs out with her friends, and likes to paint her nails and listen to music, but it feels like nothing special is ever going to happen. As a change of pace, Kana and her friends decide to design a bottle rocket and launch it into space, even though it might not get there at all. However, just when the rocket is completed, a robot suddenly crashes into and destroys it, shortly followed by a pink-haired woman claiming to be a Galactic Investigator. Kana's life quickly becomes more exciting than she ever imagined, dealing with new feelings, changing friends, and even boy troubles. It turns out life can go by in the blink of an eye, fast enough to even miss it, so what's with these weird robots that seem to show up at the worst times?!