Leo (a.k.a. Kimba in the U.S.) is a young ambitious lion cub who takes his father's place as emperor of the jungle when is father is killed by poachers. Even though his father's fate was met by the hands of humans, Leo is one of the few animals in the Jungle that doesn't fear or feel hatred toward humans. He is not alone either, he is guided by friends of his father to help create the best animal kingdom there can be.

Deep in the dark recesses of the UnderNet, Forte sleeps as he drifts aimlessly. In this cybernetic graveyard, a pulsating power re-awakens Forte, alerting him to a dangerous being shortly ahead. A haunting face appears amidst a massive bright purple blob, laughing directly at Forte. Cursing him, Forte finds himself powerless as the blob takes form, and captures him within its grasp! Nearing the time of sunset, a peaceful city and its people go about their everyday business. Curious bystanders on a sidewalk glimpse a shimmering purple light, which suddenly expands into tall pillar that reaches up to the sky. Screams erupt from the people as the pillar of light takes flight, absorbing everything in its destructive path. A tower clock dings the hour of 4 o'clock as the pillar desintigrates, leaving behind a trail of cybernetic residue and utter emptyness. 'The Program of Light and Dark'

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.