This story takes place a few months after the events of the first anime. All the EM Viruses have disappeared and the Earth is at peace. However one day viruses unlike those seen before, and two mysterious men attack the museum where the artifact, Sword of Zerker, is held. These men are Hyde and Rich Dotcom with their UMAs. They fight with each other over the artifact, only resulting in Omega-Xis accidentally swallowing it. Later, Geo Stelar meets Dr. Vega and she informs him of the continent of Mu and the OOPArts. Rogue arrives and attacks Geo and Omega-Xis to take the OOPArt. They are quickly defeated, but Vega manages to drive Rogue off with an EM weapon.
Vega then requests that Geo and Omega-Xis find the other OOPArts and prevent Rich Dotcom, Hyde and Rogue from getting them. While traveling across the world in search of the artifacts, Mega Man finds himself frequently struggling with his adversaries, while also discovering that he needs to master his new Thunder Zerker form, granted by the OOPArt. Eventually, Rich Dotcom and Yeti get their hands on the Rock of Saurian, whilst Hyde and Phantom claim the Star of Ninja. A three-way struggle ensues between them in attempts to claim the other OOPArts, but eventually it is revealed that Doctor Vega wants the OOPArts for herself to resurrect Le Mu.
Hollow then proceeds to extract the OOPArts from Yeti Blizzard and Dark Phantom. Due to the three OOPArts resonating with each other, the portal to Mu is opened. Hollow and Vega enter the portal, closely followed by Mega Man and Harp Note, who want to stop Le Mu from resurrecting. Dark Phantom and Yeti Blizzard also follow Vega, having been promised eternal life. There, Hollow takes the final OOPArt from Omega-Xis after he terminates EM Wave Change to spare Geo from Hollow's attacks. As Vega proceeds with the resurrection of Le Mu, Geo and Harp Note find Rogue, who was also tasked with the mission of preventing the reappearance of the Mu continent. Geo eventually finds Omega-Xis, changes to Mega Man, and attempts to stop Le Mu's resurrection by removing the OOPArts. This results in the three OOPArts resonating with him, transforming him into Thunder Zerker, then briefly to Zerker Ninja and Zerker Saurian, ending with Tribe King. Hollow attempts to stop him, but a single blow from Tribe King kills him.
With Le Mu being resurrected, Mega Man, Harp Note, Yeti Blizzard and Dark Phantom escape through the portal back to Earth. However, the portal grows larger as Le Mu attempts to crawl through to the other side. At this moment, Rogue appears, commanding Mega Man to destroy the portal as he holds off Le Mu, sealing him with it for good. Mega Man does so using Czar Delta Breaker, sealing off the continent, with Le Mu and Rogue. Once again, the Earth is safe. Some time later, Geo, his mother, Luna, Bud, Zack, Pat and Copper go to see Sonia's concert, during which, Omega-xis shows Geo that all the FM-ians from the original series (and their hosts) are also there.
- Judging from the opening, it appears that Capcom had initially planned for the appearance of the Wood Ninja and Fire Saurian transformations, but were forced to end the show early. Should the show have continued, these transformations and other Double Tribes may have had a chance to appear also.
|Mega Man Star Force series|
| Geo Stelar (Omega-Xis • Mega Man) • Sonia Strumm (Harp • Harp Note) • Bud Bison (Taurus • Taurus Fire) • Luna Platz (Ophiuca/Vogue • Queen Ophiuca) • Zack Temple (Pedia) • Solo (Laplace • Rogue) • A.C. Eos (Acid • Acid Ace)|
Patrick Sprigs (Gemini • Gemini Spark) • Hyde (Phantom • Dark Phantom) • Aaron Boreal • Bob Copper • Hope Stelar • Kelvin Stelar
| Mega Man Star Force • 2 • 3|
Shooting Star Rockman: Wave Change! On Air! • Rockman.EXE Operate Shooting Star
| Mega Man Star Force • Shooting Star Rockman Tribe |
Rockman the Shooting Star • Rockman the Shooting Star Tribe
Shooting Star Rockman 3 • Shuugeki On-Air!! Shooting Star Rockmeen!
| Battle Card • BrotherBand • Link Power • EM Being • EM Wave Change • Planet AM • Planet FM • OOPArts • Dealer • Satella Police|
Transer • Star Carrier • Hunter VG • Visualizer • Star Break • Tribe On • Noise Change
Wave Scanner • Wave Command Card • Noise Kaizou Gear