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.

On her way to school one day, Suzume Iwato stumbles upon Souta Munakata, a young man searching for abandoned areas. The high school girl directs Souta to a nearby ruin, but out of pure curiosity, she herself decides to head to the same destination. Once there, Suzume discovers an isolated door with a dreamlike universe lying beyond it—a place that she can see and feel, but not enter. A strange stone rests on the ground nearby, but it turns into a cat-like creature and scurries away when Suzume lifts it. Suddenly afraid, she heads back toward her school, not realizing that her act of leaving the door open will have consequences. With the keystone released, the evil within the other universe can now freely escape and wreak havoc throughout Japan. Intending to correct her dangerous mistake, Suzume joins Souta—whose true goal is to prevent evil from festering—in finding and locking all open doors before the country is destroyed.

Although Jirou Horikoshi's nearsightedness prevents him from ever becoming a pilot, he leaves his hometown to study aeronautical engineering at Tokyo Imperial University for one simple purpose: to design and build planes just like his hero, Italian aircraft pioneer Giovanni Battista Caproni. His arrival in the capital coincides with the Great Kanto Earthquake of 1923, during which he saves a maid serving the family of a young girl named Naoko Satomi; this disastrous event marks the beginning of over two decades of social unrest and malaise leading up to Japan's eventual surrender in World War II. For Jirou, the years leading up to the production of his infamous Mitsubishi A6M Zero fighter aircraft will test every fiber of his being. His many travels and life experiences only urge him onward⁠—even as he realizes both the role of his creations in the war and the harsh realities of his personal life. As time marches on, he must confront an impossible question: at what cost does he chase his beautiful dream?

Middle school student Mirai Onozawa is dissatisfied with her family circumstances and, in a moment of frustration, wishes to tear everything apart. Unfortunately, these destructive thoughts seem to come true in the form of a magnitude 8.0 earthquake just a few moments later. When summer vacation begins, Mirai reluctantly takes her younger brother Yuuki to Odaiba, where a robot exhibition that he wanted to go to is being held. However, while they are in the exhibition center, the fury of a major earthquake shakes the Kanto region; helpless, both kids witness the devastating power of this natural disaster as it brings the city to its knees. In its aftermath, they stumble upon Mari Kusakabe, a motorcyclist and single mother who decides to help the young siblings. Aiming to return to their homes and reunite with their families, the group sets off on a long and hard journey through the decimated city.