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.

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.