Season 1 of Wonder Beat Scramble premiered on January 2, 1986.

In 2119, the spaceship Green Sleeves found 3 planets attacked by X23, a moving planet heading Earth. The Earth government ordered Green Sleeves to attack X23, but Dr. Sugita, the captain of Green Sleeves, refused because he believed they could co-exist. Then, the communication with Green Sleeves was cut abruptly...

In 2121, Susumu, the son of Dr. Sugita, is visited by strangers. The take him to Dr. Miya, one of the few supporters to Dr. Sugita's decision, while most blamed him as a traitor. Dr. Miya recommends Susumu to join White Pegasus, a team of special medical recuers. Their Micronizer System can shrink human so that they can cure from the inside of the body. Shortly afterwards, X23 has come in visual range at last. Hues - the aliens of X23 - choose Susumu's friend as their first target. Susumu and the other members of White Pegasus manage to defeat Hues inside of his body. But Susumu finds the signals emitted from the chips within Hues are the music composed by himself and his mother, as a gift to Dr. Sugita...