Three middle school students known as the Small Three accidentally open a gateway to a parallel universe and must rescue one of their younger sisters after she is kidnapped by alien invaders. Pyontaro Tezuka lives with his adoring little sister, Futaba, in a world that looks like a simple, cartoonish drawing. Along with his neighbors and best friends, Hiroshi Ochanomizu and Tsubame Azuma, he is given a mysterious disc by their teacher. When the boys play the disc on a video game console, a lifelike, hyper-realistic world appears on the screen, and a dragonfly emerges from the television. Futaba chases the creature and is pulled into the alternate dimension, only to be captured by the alien forces that have conquered this version of Earth.

The trio follows Futaba into the parallel world and makes two startling discoveries. First, the landscape and cities are identical to their own, but rendered in gritty, realistic detail. Second, their own bodies retain their cartoonish, chibi-like appearance, which grants them superhuman strength, speed, and invincibility in this reality. This contrast allows them to survive falls from great heights and withstand attacks that would be fatal to ordinary humans. As they search for Futaba, they encounter human resistance fighters and learn that the alien occupation has brought humanity to the brink of disaster. The trio decides to join the fight, adopting the name Thunder 3 as they battle the extraterrestrial threat.

A major turning point occurs when the alien forces deploy a devastating superweapon that wipes out every human on the planet except for those living in Japan. Faced with the near-extinction of humanity, the Thunder 3 intensifies its efforts to rescue Futaba and stop the invaders. Their journey involves forming alliances with sympathetic aliens whose own homeworld was destroyed, as well as coordinating with a rebel group called Rebellion. The story blends moments of dark, large-scale science fiction action with the humor and visual oddity of seeing cartoon-like protagonists navigate a world that looks like live-action photography. The series builds toward a climactic confrontation as the Thunder 3 fights not only to save one girl but to reclaim an entire conquered Earth.