Next Episode of Thunder 3 is
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Unremarkably ordinary middle schoolers, Pyontaro, Hiroshi and Tsubame, wander into an extraordinary adventure when Pyontaro's little sister goes missing.
Pyontaro, Hiroshi and Tsubame — the Small 3 — load up an odd disc from their teacher. When they're not looking, Pyontaro's little sister Futaba vanishes.
Stranded in a new world, the Small 3 realize they have incredible powers. They meet other versions of themselves and learn how this reality differs.
Futaba, held captive by aliens, is attacked with a heat ray gun inside the spaceship. However, she remains unharmed and wanders around the spaceship. Meanwhile, Small 3 goes to Doc in the "Multiverse" to get clues about Futaba's whereabouts. Just then, he spots a parent and child in the city being held at gunpoint by aliens.
As college student Segami struggles with his dystopian world, a hot schoolmate hands him an enticing flyer. Hoping to meet girls, he finds something else.
With his mind in a whirl, Segami runs into the Small 3. They witness a bold fighter pilot pit his life against an alien ship. Will it light a fire?
While imprisoned in a spaceship, Futaba encounters a mysterious life form named Kyu-chan and they begin to act together. Meanwhile, on Earth, the "Rebellion" begins its guerrilla warfare against aliens in the Shibuya Mission. Segami, nervous about using unfamiliar equipment and firearms, receives the secret weapon "Tsuyokunaru" from former SAT member Sumeragi and heads to the battlefield.
Aliens surround a sleeping Futaba! In Shibuya, Segami and his comrades fight fiercely but lose ground. As he retreats, he spots Tashiro under attack.
Futaba faces off against a squad of alien soldiers to protect her new friend. Facing heavy losses, Segami and the Rebellion turn to their secret weapon.
Genius commandeers an alien walker and leads a counterattack. But two fearsome alien soldiers are en route. Meanwhile, Doc and the others seek answers.
As the Small 3 soar toward Shibuya, Genius runs out of options against a relentless alien warrior. Reinforcements arrive — but will it be enough?
The Small 3 finally touch down in Shibuya. As they unleash their power against giant aliens, a livestreamer broadcasts their fight to the world.
Pyontaro, Tsubame, and Hiroshi had subdued the aliens. Immediately afterward, a laser beam was fired from the flying battleship above, hitting Tsubame directly. Seeing his comrades attacked right before his eyes, Pyontaro gave in to his emotions and charged at the flying battleship, crying. Miraculously, that battleship was where Futaba was being held captive.
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