The game opens with a shot of the starry skies, and an unusual big red shooting star, and two mysterious characters talking about the coming of the end. Some time after, Geo is in his class room, as he and the rest of his class update the Star Carrier into a Hunter-VG, a more upgraded version of the Star Carrier, and allowing the use of Wizards, EM Beings who can appear anywhere, without the need of Visualizer to see, and are made of Real Wave. A new student join the class, Jack, and his sister as a teacher, Ms. Tia, the same people from the beginning of the game. Geo is told by Luna, who wants to be class president once again, to look for people in need of help, and he eventually meet Woody, the head of the Science Club at school, who wants to launch a rocket into space using his Wizard, Magnes. Woody asks Geo to get him a special card, which is only available from a tournament in Spica Mall. At the same time, a mysterious man is following Geo and tells him he knows his identity as Mega Man, which surprises Geo, and tells him he can get the card if he shows up at Spica Mall to fight him as Mega Man.
At Spica Mall, Geo is late due to a malfunction in the security system, only to find out the mysterious man, known as Ace, a Satella Police officer, defeated all of his opponents in mere seconds with his Wizard, Acid, who are able to EM Wave Change together into Acid Ace. Geo and his friends get the card from Ace, who says he'll check Geo's fighting skills in another time, and they all prepare to the rocket launch the next day. That night, Jack and Tia appear at school and infuse Magnes with a Noise Card - which uses the Noise (a by-product of Wizards) to corrupt Wizards, thus creating Spade Magnes. The next day, before the rocket launches, the rocket malfunctions and threatens to destroy whole Echo Ridge, but eventually stopped by Mega Man. After Spade Magnes' defeat, a large amount of Crimson is created, and flys from the battlefield to an unknown destination.
Some time after, Sonia Strumm arrives in Echo Ridge and asks Geo and his friends to come to WGB Studios, to be extras on the show she is on. They are all excited, but Geo meets Ace at the park before going to the Studios the next day. Ace gives him the Ace Program/Joker Program (which depends on the version the player is playing), which allows Mega Man to harmonize with the Noise, even though it is dangerous to EM Beings to be near large amount of Noise.
At WBG Studios, Geo meets Belle and her Wizard, Ice, who is obsessed with getting Belle more screen time, despite Belle not wanting to.While shooting, Jack infuse Bud with a noise card, which wakes up Taurus inside of Bud, and Mega Man must fight the rampaging Taurus Fire. After the incident, Taurus apologizes to Bud, asking him to be his Wizard, and giving Bud the ability to EM Wave Change.Later, Jack and Tia corrupt Ice too and she becomes Diamond Ice, who freezes the event stage Sonia is playing on, and was created by Lee Stern, a WGB Studio employee who is an expert on creating Real Waves. After Mega Man defeats Diamond Ice, the gang hears Sonia's new song (which is the game's theme song, and lyrics appears in the game but are not heard).
Some time later, Ace reveals to Geo that the red shooting star he sees is called Meteor G, a huge meteor made out of Noise, and is controlled by an organization called Dealer, who plan to crash it down into Earth to destroy all EM Wave technology.
While traveling to their school's trip in Alohaha, a beautiful island which is covered in EM Environmental System which prevents any natural disasters from happening, Mega Man takes the Astro Wave to get there on time, but encounters Dark Phantom, who wants Mega Man's Ace/Joker Program. Though able to defeat him, Mega Man is overwhelmed by Noise, but is suddenly able to control it, and even Noise Change. Dark Phantom flees, and Mega Man continues to Alohaha.
At Alohaha, Geo meets the EM Environmental System's Wizard, Strong, but he is eventually corrupted by Dealer as well, making him Club Strong. After the fight, Mega Man decides to follow the Crimson which appeared, and is lead to the beach, where he finds out the ones collecting the Crimson were Jack and Queen Tia, and they also have FM-ians with them, Corvus and Virgo (respectively). They both EM Wave Change, and Jack Corvus decides to fight Mega Man (in a fixed fight, the player must survive 3 turns). After the fight, Mega Man is exhausted, and a mysterious tall figure named Joker appears, telling Jack and Tia that Mr King, Dealer's leader, decided they do not need to fight Mega Man yet, and Luna shows up looking for Mega Man. She is attacked by Joker but Mega Man defends her, only to be fooled by Joker, which uses Dread Lazer to delete Luna.
Geo is crushed and mourns Luna, but Ace contacts him, telling him they can still restore Luna, by using Dr. Goodall, a scientist of WAZA, and with Acid's Frag search. After Geo founds all of Luna's Data Frags, Dealer launch an attack on WAZA HQ, sending waves of copies of Omega-Xis at them, as Mega Man and Omega-Xis must defend against until Dr. Goodall charges her super weapon, a Noise Jammer, which disables low-level(like the clones) EM Bodies within its range. After the successful defense, Mega Man finds out that Dark Phantom has gotten into WAZA HQ, and has kidnapped Taurus Fire and Harp Note, but Mega Man defeats him, which causes Dark Phantom to become confused, and he stumbles from the Cyber Core road, into the abyss.
After the battle, Geo finds out Acid Ace fights Queen Tia's EM Wave Change, Queen Virgo, but Acid forces him to quit the EM Wave Change because he has reached critical levels of radiation which are lethal to Ace. Ace reveals he was part of Dealer before becoming a Satella Police Officer, and that he liked Tia, and wishes she would leave Dealer to join him. Though powerless, Ace asks Mega Man to fulfill his wish, and Mega Man fights and defeats Queen Virgo, which leads to the arrest of Queen Tia. Dr, Goodall is then able to bring Luna back using the data Geo found.
Jack, learning his sister was arrested, is furious, and disobeying Mr. King's orders, he goes to Echo Ridge Elementary and unleashes a fury attack on the election day, where Luna and the rest of the school is. Although no match to him, he is stalled by the School's gardener, Damian Wolfe and his EM Wave Change, Wolf Woods. Geo rushes to school, and finds Zack, Luna and Bud in the class, and Solo with them. Jack Corvus unleashed a large amount of Noise-corrupted Wizards in school, and Geo and his friends are unable to exit the normal way, so Solo cracks open a huge hole in the floor for them to drop (although Zack stays behind), and using the Noise Wave, Mega Man and Rogue fight together the Strong Noisms at the Noise Waves and before reaching to the roof, Rogue challenges Mega Man to a fight and loses, and as Geo proceeds to Jack Corvus' fight, Luna tries to reason with him, but fails. Mega Man defeats Jack Corvus in front of everyone at school, and Jack falls unconscious.
Mr. King, losing two of his agents, believes the only ones still on his side is Joker and his right hand, Heartless. While Geo and Ace are looking for clues where many Noise Wizards went rampant on, Joker shows up and reveals his powers are also able to control Acid, which turns Acid Ace into his finalized form, Acid Ace Illegal (or Black Acid Ace). Mega Man is able to hold out for enough time for Acid Ace's EM Wave Change to fade, but Ace is physically exhausted and is taken to the hospital.
Mr. King decides to show the Earth the power of Meteor G and uses it's ability, called Dread Lazer (the same as Joker's) to create Noise around WGB Studios and WAZA HQ, thus trapping Belle, Lee and Dr. Goodall, but they are saved by Mega Man.
The Satella Police decides to raid Dealer's base, and discovers it is a Crimson factory. After reaching Dealer's main room, Mega Man confronts Joker, but Ace shows up and Joker again finalizing Acid Ace, and Mega Man fights and defeats Acid Ace. After the fight, Acid Ace tells Mega Man he regained his senses, but knocks Mega Man out, and proceed to Mr. King's room. Mega Man wakes up, and rushes to Mr. King's room as well. He sees the unconscious Ace, and Joker standing on top of him. Mega Man fights Joker, who is revealed to be an Mr. King's Wizard, and uses his finalized form, Dread Joker to fight Mega Man. Jack and Tia shows up to confront King, but he orders Joker to use his self-destruct, and escapes alone, as Heartless reveals herself as a spy for the WAZA. Joker is about to self-destruct, but Ace EM Wave Changes again into finalized Acid Ace on his own, and fights off Joker, sharing the explosion with him, deleting himself but the others are saved.
Geo is invited to the Orbital Base by Heartless, who tells him she was able to stall Meteor G's course to Earth, with the aid of none other than Kelvin Stelar, Geo's father, who is inside Meteor G. Jack and Tia shows up and tell Geo they plan to reset the course to Earth, destroying 80% of Earth's population as well. They reveal they are the prince and princess of a country who was advanced in EM Wave technology, but was wiped out due to the other countries will to take the technology to themselves. They were left alone, but were picked by Mr. King and to his organization. They go to the Meteor Control Cyber Core, and although Mega Man catches up with them, they have already set Meteor G's course.
Geo and the staff of WAZA HQ, as well as Lee Stern and Woody, meet up and discuss what they should do, saying Meteor G will crash to Earth in 12 hours, but Heartless reveals that due to Kelvin's power, he is able to stall the meteor for at least 24 more hours, and WAZA decides to launch Mega Man into the red shooting star to destroy Meteor G using Woody's space rocket, and Lee building Real Wave barrier to protect the rocket until it reaches Meteor G.
