A goldfish sneaks away from home and floats off on the back of a jellyfish. After getting stuck in a glass jar, she drifts to the shore where she is freed by Sousuke, a five-year-old boy who lives with his mother Lisa in a house by the sea while his father Koichi works on a fishing boat. After healing a cut on Sousuke's finger by licking it, the goldfish is named Ponyo by her new friend.

Unknown to Sousuke, Ponyo already has a name and a family. Her father Fujimoto, a sorcerer who forsook his humanity to live underwater, searches frantically for his daughter Brunhilde. When found and captured, Ponyo rejects her birth name and declares that she wants to become a human. Using the power received from Sousuke's blood, she grows arms and legs and escapes to the surface once more. But the magic released into the ocean causes an imbalance in nature, causing the Moon to start falling out of orbit and the tides to grow dangerously stronger. Reunited with Ponyo, Sousuke must pass an ancient test to restore order in the world and let his companion live on as a human.

In a world plagued by magical dangers and threats, there exist special warriors—known as Inquisitors—who are tasked with non-violently preventing these threats and nefarious actions. The Anti-Magic Academy is a specialized school built to educate and train these Inquisitors, which splits its students into small squads in order to train them to work together. Among these talented squads is the 35th Test Platoon, also known as the "Small Fry Platoon" due to its low ranking and incompetent members. However, everything changes when Ouka Ootori, a powerful yet rebellious former Inquisitor, is forced into joining due to her tendency to break rules and committing a serious violation: the killing of a witch. Tempers flare upon her arrival, as she clashes with their clumsy captain Takeru Kusanagi and argues with the rest of the squad over her views on witches. This eclectic group has a long way to go if they wish to succeed and climb the ranks at the Anti-Magic Academy: they must first set aside their differences and come to work together as a team. [Written by MAL Rewrite]

Deep in the Ararat Mountains of Turkey, a secret organization known as ARCAM has found what is believed to be Noah's Ark. However, the U.S. Machine Corps., a rogue organization of the Pentagon, wants to take over the Ark as a means of global supremacy. Only a special ARCAM operative known as a Spriggan stands in their way. Japanese Spriggan Yu Ominae teams up with French Spriggan Jean-Jacques Mondo to combat members of the U.S. Machine Corps. led by Col. MacDougall—a genetically-enhanced boy with deadly psionic powers. However, they must act fast and stop MacDougall before he uses the Ark for his own agenda.

On his first day of high school at the formerly all-girl's Ousai Private Academy, Takatoshi Tsuda is called out for his untidy uniform by the student council president Shino Amakusa. In apology for delaying Takatoshi for his first class—and stating that the group needs a male point of view to accommodate the arrival of boys at the school—Shino offers him the position of vice president of the student council. Though unwilling, Takatoshi finds himself appointed as the newest member of the student council having yet to even step foot inside the school building. Takatoshi soon realizes that the other student council members who are more than a little strange: President Shino, who is studious and serious in appearance, but actually a huge pervert, fascinated with the erotic and constantly making lewd jokes; the secretary Aria Shichijou, who may seem like a typical sheltered rich girl, but is just as risque as the president, if not more so; and finally, the treasurer Suzu Hagimura, who may act fairly normal, but has the body of an elementary school student and is extremely self-conscious of it. Surrounded by these colorful characters, the new vice president must now work through a nonstop assault of sexual humor and insanity. [Written by MAL Rewrite]