Netto's father Yuuichirou Hikari has made a scientific breakthrough by introducing the "synchro chips". If an operator and his or her navi are in a special enviroment known as a "dimensional area", they can fuse together in the real world via a technique called "cross fusion"! Yuuichirou's first test subject, Misaki Gorou, attempts the process and sadly fails. Netto offers to try with Rockman, but his father forbids it. Cross Fusion puts enormous strain on the operator's health, and battling in the real world could mean death.

Trill, a mysterious navi said to have originated from the world of Beyondard, is discovered. And new beast-type enemies, the Zoanoroids, want him for his special power. Netto Hikari and Rockman must protect their new friend while they try to figure out what Trill is really and his connection to the two legendary cyber beasts, Grega and Faltzer.

In the year of 20XX, a young boy by the name of Netto Hikari receives a very special gift as he enters the 5th grade. His very own customized net navi, Rockman! Despite Rockman's small size and far more responsible personality, the two boys quickly become the best of friends. A net navi is designed to guide his operator from the inside of his or her PErsonal Terminal, or simply PET for short. Children and adults alike enjoy friendly "Net Battles", where they spar their navis against each other to prove their worth.

In the year 220X, the world has advanced toward radio-wave technology, and the world is connected through the Wave Road. Meet Subaru Hoshikawa, a fifth-grade student who lost his father in a space accident. Subaru meets an extraterrestrial radio-wave being named War-Rock, descending from a distant FM planet. War-Rock claims to know about Subaru's father, but many alien beings are after War-Rock. The two work together and merge into Rockman, a radio-wave human capable of traversing the Wave Road and battling the radio-wave viruses and FMs that threaten the Earth.