The year is 220X. Technology has advanced rapidly since the age of the internet, leading to the creation of new and more efficient modes of transportation, as well as the construction of futuristic cities, all linked together by three satellites orbiting the Earth—Pegasus, Leo, and Dragon. The satellites accomplish this by maintaining a network of EM waves around the planet's atmosphere, thereby powering the invisible EM Wave World. The human population carries portable devices called Transers to interface with the EM Wave World and other electronic devices. Problems caused by criminals and EM Wave Viruses manipulating the EM Wave World are commonly dealt with by the Satella Police.
A new breed of radio wave viruses have substantiated at a museum, so Subaru investigates. While there, he notices a strange aura emitting from a display item called the "Sword of Berserk." Soon after, two new enemies appear and begin to battle one another for the sword. In the heat of the struggle to protect the sword, War-Rock accidentally ingests it, and the enemies flee.
After discussing the incident with Misora, Subaru meets a professor named Orihime. She explains that Cepheus's activity on Earth recently awakened the EM wave residents (UMAs) of the lost continent Mu. Mu was sealed with an extremely powerful EM wave being within it, and the UMAs wish to break the seal in order to release the being. But to do so, they require three ooparts—one of which is the sword stuck in War-Rock's stomach—and Orihime hopes to cooperate with Subaru in order to retrieve the ooparts first. Suddenly however, a mysterious new enemy named Burai attacks the university and assaults Subaru...
Rockman and Burai battle, but Burai is eventually forced to retreat after Orihime intervenes with a large jamming beam that disrupts EM wave activity. Later, Subaru takes War-Rock to AMAKEN to have the sword extracted from his stomach, and in the meantime, he and his friends play a materialization hammer game using the Star Carriers
Subaru explains the quest for the ooparts to Misora, who expresses interest in helping. Burai attacks again, and the duo transform into Rockman and Harp Note to fight. Burai attempts to take the Sword of Berserk, but Rockman suddenly uses it to transform into the Thunder Berserk form, and defeats him.
Orihime sends Subaru to the snowy mountain range of Himanala to locate an oopart. There, he meets a village girl named Lana who assists him in his search. She also tells of a yeti that has been terrorizing the village recently. Upon further investigation, Subaru encounters Yeti Blizzard, but he escapes amidst their battle.
Rockman's quest for the oopart deepens as he begins to explore the ruins in the Himanalas. Yeti Blizzard tails him, hoping to swipe the treasure for himself, and Harp Note also appears to aid Rockman. In the end, there was no treasure, and Yeti Blizzard is defeated in an inevitable confrontation with the heroes.
Subaru receives word from Orihime of an oopart hidden in a pyramid. Meanwhile, a painter named Hyde recalls when he first met his UMA partner, Ghost. Together, they are also traveling to the pyramid. Rockman explores the pyramid with hesitation, but eventually meets Hyde inside. Hyde transforms into Phantom Black, and Rockman counters with Thunder Berserker, but the sword is out of control!
The sword causes Subaru to retreat, allowing Phantom Black to peacefully investigate the pyramid alone. To make matters worse, Burai soon appears and knocks Rockman unconscious. Within Subaru's psyche, he encounters the sword thrust into the ground. In an allusion to The Sword in the Stone, Subaru is able to pull the sword from the ground, awaken, and take control the Thunder Berserk form to defeat Burai. Meanwhile, Phantom Black finds that, unfortunately, the pyramid holds no treasure.
There's been a lot of buzz at Dombra Village about a lake beast nicknamed Dossy (a parody of Nessie), so Subaru travels there out of curiosity. He encounters a television director named Gerry Romero who is secretly gathering data on the beast. Furthermore, he runs into Monjirou Gori (the partner of UMA Yeti). Gerry is eventually pursued by a UMA and transforms into Plesio Surf, defeating both Yeti Blizzard and Rockman before retreating.
Subaru and Misora discuss recent events when they meet the UMA Brachio. Brachio has been trying to protect the lake from intruders and pollution, and he had attacked Rockman in error. However, Gori commands a group of workers to begin filling in the lake, enraging Brachio Wave and causing him to attack them. Rockman and Harp Note intervene, giving Gori the opportunity to submerge to the lake's bottom and steal the oopart hidden below.