Haru Shinkai, a Junior High Student discovers an Appmon, which reveals himself to be Gatchmon and they become partners. Together, with other members, they plan to stop an artificial intelligence, Leviathan, from taking over humanity's.

In the year 2045, technology has finally evolved to a degree of prosperity for the world. The World Wide Web has become a world for "App Monsters" or "Appmons", an artificially intelligent beings born within mobile apps. The series focuses on Haru Shinkai, an everyday Junior High Student discovers an Appmon lurking in his Smartphone, which reveals himself to be Gatchmon and the two become partners. Haru also learns from Gatchmon that the artificial intelligence called Leviathan is creating viruses to turn all Appmons into evil, and the two join forces to stop them. As the series progresses, Haru gains the help of the rookie idol Eri Karan, the famous AppTuber Torajirou Asuka, the prodigy hacker Rei Katsura, who is in search for his younger brother that was kidnapped by Leviathan, and Haru's best friend Yujin Ozora, each one partnered with their own Appmon to help in the fight to defeat Leviathan and restore the balance between their two worlds.