Thunder 3 manga volume 1 features story and art by Yuki Ikeda.

Pyontaro is a middle schooler whose little sister, Futaba, simply adores him. One day, he and his buddies—the so-called “Small Three”—decide to watch a weird disc their teacher lent them. Little do the boys realize this disc is linked to another universe…and while they aren't looking, Futaba gets sucked in! Can Pyontaro and his friends find Futaba? And just what is this other world they've discovered?!

Thunder 3 manga volume 2 features story and art by Yuki Ikeda.

In the parallel world, Pyontaro and his pals continue to search for a way to rescue Futaba from her alien abductors. After narrowly saving some people in town, the trio is set upon by a group of armed aliens, but then…Pyontaro unleashes a devastating attack of his own!

Meanwhile, aboard the alien spaceship, an even more fearsome alien squadron mobilizes to recapture Futaba after she escapes! And, as the alien invasion and subsequent subjugation of the city's residents takes a turn for the worse, an encounter between the Small Three and a certain man promises to turn the tides of fate!

Thunder 3 manga volume 3 features story and art by Yuki Ikeda.

Not long after Segami witnesses the self-defense forces launch a suicide attack against the aliens in a desperate act of defiance, he receives news from his mother that steels his resolve to fight as well. With the Small Three in tow, Segami joins the insurrection group rebellion, and sets out ahead of his miniature comrades to take part in the Shibuya operation - a guerrilla attack against the invaders!

Meanwhile, Futaba awakens from her slumber aboard the alien ship, only to find herself surrounded by armed soldiers who attack her without warning, forcing her to confront the alien menace at last!

Thunder 3 manga volume 4 features story and art by Yuki Ikeda.

The Shibuya mission turns into a fierce battle—but after losing many of their comrades, Segami and the other remaining members of Rebellion turn to their secret weapon “Empoweral” to make their final stand against the super-powered aliens. And, little by little, the tide of battle seems to turn in their favor…Until a new menace rears its head from among the invaders' ranks! Elsewhere, the Small Three catch wind of the fighting in Shibuya from an internet broadcast and, faced with so much death and devastation, are forced to make a choice: do they continue to search for Futaba, or make for Shibuya at once?!