In the distant future, humanity has been driven to near-extinction by giant beasts known as Klaxosaurs, forcing the surviving humans to take refuge in massive fortress cities called Plantations. Children raised here are trained to pilot giant mechas known as FranXX—the only weapons known to be effective against the Klaxosaurs—in boy-girl pairs. Bred for the sole purpose of piloting these machines, these children know nothing of the outside world and are only able to prove their existence by defending their race. Hiro, an aspiring FranXX pilot, has lost his motivation and self-confidence after failing an aptitude test. Skipping out on his class' graduation ceremony, Hiro retreats to a forest lake, where he encounters a mysterious girl with two horns growing out of her head. She introduces herself by her codename Zero Two, which is known to belong to an infamous FranXX pilot known as the "Partner Killer." Before Hiro can digest the encounter, the Plantation is rocked by a sudden Klaxosaur attack. Zero Two engages the creature in her FranXX, but it is heavily damaged in the skirmish and crashes near Hiro. Finding her partner dead, Zero Two invites Hiro to pilot the mecha with her, and the duo easily defeats the Klaxosaur in the ensuing fight. With a new partner by his side, Hiro has been given a chance at redemption for his past failures, but at what cost?

After the destruction of their hometown, childhood friends Kafka Hibino and Mina Ashiro make a pact to become officers in the Defense Force—a militarized organization tasked with protecting Japan from colossal monsters known as "kaijuu." Decades later, the 32-year-old Kafka has all but given up on his dreams of heroism. Instead, he cleans up the remains of the slaughtered kaijuu after they are defeated by valiant soldiers—including Mina, who has successfully achieved their shared goal. Upon meeting his new coworker, Reno Ichikawa, Kafka faces a mirror of his past self: an ambitious young man whose one desire is to fight as a member of the Defense Force. Unfortunately, the two are soon involved in a freak encounter with a rogue kaijuu. Though Kafka demonstrates his innate heroic nature and rescues Reno from certain doom, he is left gravely injured. While both men recover in a hospital, Kafka is seemingly attacked by another one of the beasts. As a result, he gains the ability to transform into a humanoid kaijuu with the strength and powers of the massive monsters menacing Japan. Dubbed "Kaijuu No. 8" by the military, Kafka resolves to use his newfound gifts for the greater good. Tied together by mutual respect, Kafka and Reno set out to join warriors like Mina at the forefront of the Defense Force.

Mary Smith is a clumsy girl with wild red hair who can't seem to do anything right. After moving in with her Great Aunt Charlotte, Mary finds herself lonely and bored, until one day she spies a cat which seems to keep changing color every time she sees it. Curiosity gets the better of her and she follows it into nearby woods. Deep in the forest, the cat takes her to a clearing with dead trees and brown grass, where the only sign of life is a cluster of mysterious blue flowers that Mary has never seen before. The gardener of the estate later tells her that the rare species is called "Fly-by-Night," and is said to be sought by witches for its incredible magical power. When the strange cat returns to her one night, Mary is led once again into the woods, but this time to an old broomstick hidden by a gnarled tree. After she clumsily squashes some Fly-by-Night against the broomstick, it begins to glow, whisking her off into the sky. Her wayward journey ends at the Endor College for Witches, where she is mistaken for a new student. And so, Mary must learn to look after herself in this marvelous new world of magic, where things are not always as they seem.