電波によるテクノロジーが発達した未来。人類はその技術を利用し、遥か遠い異星の知的生命体とのコンタクト計画を進めていた。主人公、星河スバルは宇宙飛行士の父を持つ少年。ある時スバルの家に父の後輩・天地が訪ねてくる。天地が差し出したのは父、大吾が開発したというメガネ、ビジライザーだった。

登校拒否を続けているスバルの家に、クラス委員長の白金ルナが訪ねて来る。ルナから逃げ出したスバルは、ビジライザーを通してぶつかり合う謎のふたつの光を目撃する。

スバルが見た光の正体は電波の体を持つ異星人ウォーロックだった。自分のトランサーの中にウォーロックをかくまうことになったスバル。ウォーロックと共に街へ出かけたスバルは電波ウイルスが引き起こす事件に巻き込まれてしまう。

ウォーロックと合体して電波人間に変身したスバルはウォーロックに言われるまま電波ウイルスとのバトルに突入する。電波空間内での体験に戸惑いながらも、必死で戦うスバルだが･･･

ロックマンに変身したスバルは電波ウイルスを倒すため、電波空間を駆けめぐっていた。一方、天地の後輩、宇田海は周囲に隠れてある研究を進めていた。

自分の発明を他人に奪われるのではないかと疑心暗鬼に駆られた宇田海は、FM星人キグナスに取り付かれてしまう。宇田海とキグナスは合体し、キグナス・ウィングに変身する。

キグナス・ウイングとロックマンはＡＭＡＫＥＮ内で激しい戦いを繰り広げる。だがバトルの最中、キグナス・ウイングは手下を放ち姿を消してしまう。キグナス・ウイングが向かったのは宇宙空間だった。

ウォーロックは学校に興味を持ち、スバルに学校に連れて行けと口うるさく要求する。仕方なく学校へ行くことにしたスバル。委員長のルナは大張り切りでスバルの世話を焼く。

オックスはゴン太と合体してオックス・ファイアに変身、学校内を破壊しはじめる。スバルはロックマンに変身してオックス・ファイアと戦う。そんな中、ルナがオックス・ファイアに捕えられてしまう。

乾山深夜、自分にしか聞こえない音色に誘い出されたウォーロックは新たなＦＭ星人ハープと出会う。ハープは人間の少女と合体してハープ・シンガーと名乗りウォーロックを倒そうとする。

アイドル歌手・響ミソラのバーチャルライブが開催されることとなり、スバルはルナたちに強引に誘われしぶしぶ会場へ向かう。だが、ステージ上のスクリーンに現れ歌い始めたのはハープシンガーだった。

度重なる電波ウイルス事件に、スバルが何か関わっているのではないかと疑う五陽田はスバルを監視しはじめた。困惑するスバルだが･･･

Geo meets Mitch Shepard, a science teacher, and a classmate, Pat Sprigs. He attends one of Shepard's classes and becomes excited about making bottle rockets for the next session. However, that night, the FM-ian Libra appears and Mega Man injures him in battle. Libra escapes into Shepard's Transer and takes over his body, hiding until his injury heals. He then tries to live Shepard's life normally, but the suspicious activity attracts Geo's attention. The two end up battling when Libra transforms into Libra Scales, but because of his injury, he is easily defeated and Shepard is returned to normal.

Geo meets Mitch Shepard, a science teacher, and a classmate, Pat Sprigs. He attends one of Shepard's classes and becomes excited about making bottle rockets for the next session. However, that night, the FM-ian Libra appears and Mega Man injures him in battle. Libra escapes into Shepard's Transer and takes over his body, hiding until his injury heals. He then tries to live Shepard's life normally, but the suspicious activity attracts Geo's attention. The two end up battling when Libra transforms into Libra Scales, but because of his injury, he is easily defeated and Shepard is returned to normal.

Everyone in Echo Ridge is laughing uncontrollably, and Omega-Xis suspects the FM-ian Gemini. Soon after, Mega Man encounters Gemini Spark and learns that when Gemini fuses with a human, he separates into two very powerful entities. The audience learns that Pat is said human, and he continues to manipulate people's emotions (now making them inconsolably angry) to lure Geo back into battle. The episode ends on a cliffhanger with Mega Man and the two Gemini Sparks engaging in another heated battle.

Everyone in Echo Ridge is laughing uncontrollably, and Omega-Xis suspects the FM-ian Gemini. Soon after, Mega Man encounters Gemini Spark and learns that when Gemini fuses with a human, he separates into two very powerful entities. The audience learns that Pat is said human, and he continues to manipulate people's emotions (now making them inconsolably angry) to lure Geo back into battle. The episode ends on a cliffhanger with Mega Man and the two Gemini Sparks engaging in another heated battle.

The battle between Mega Man and both Gemini Sparks rages on, eventually taking to the sea itself. While Mega Man manages to get the upper-hand a few times, he is ultimately defeated. Before Gemini Spark can deliver the finishing blow, Lyra Note intervenes as a distraction, and Mega Man is spared. Then, young Claud Pincer is obsessed with Sonia Sky but is unable to get into a concert. The FM-ian Cancer fuses with Claud while trying to target a muscular bodyguard instead, and he becomes depressed that a scrawny child is the one who shares his wavelength. The fusion isn't perfect, so Cancer Bubble (with Claud's mentality) rages through Echo Ridge in an attempt to get concert tickets.

The battle between Mega Man and both Gemini Sparks rages on, eventually taking to the sea itself. While Mega Man manages to get the upper-hand a few times, he is ultimately defeated. Before Gemini Spark can deliver the finishing blow, Lyra Note intervenes as a distraction, and Mega Man is spared. Then, young Claud Pincer is obsessed with Sonia Sky but is unable to get into a concert. The FM-ian Cancer fuses with Claud while trying to target a muscular bodyguard instead, and he becomes depressed that a scrawny child is the one who shares his wavelength. The fusion isn't perfect, so Cancer Bubble (with Claud's mentality) rages through Echo Ridge in an attempt to get concert tickets.

Mega Man is stuck delivering mail throughout Echo Ridge. When he makes a stop at Luna's house (who has a crush on him), she formulates a plan to try to have future meetings with him through mail deliveries. Then, Mega Man battles with a new enemy, Wolf Woods, but he flees from battle. The next day, Geo meets Damian Wolfe, a gardener who reacts oddly to round-shaped objects. Meanwhile, Damian goes on a date at a shopping mall with a woman he gardens for while Geo participates in a contest there to try to win a telescope set.

Mega Man is stuck delivering mail throughout Echo Ridge. When he makes a stop at Luna's house (who has a crush on him), she formulates a plan to try to have future meetings with him through mail deliveries. Then, Mega Man battles with a new enemy, Wolf Woods, but he flees from battle. The next day, Geo meets Damian Wolfe, a gardener who reacts oddly to round-shaped objects. Meanwhile, Damian goes on a date at a shopping mall with a woman he gardens for while Geo participates in a contest there to try to win a telescope set.

While Damian and Samantha enjoy their date in the mall, Gemini Spark finally finalizes the transformation between Damien and the FM-ian Wolf, and Wolf Woods rampages through the mall. Mega Man and Lyra Note appear to battle, but ultimately, Samantha is able to calm him down. The FM-ian Wolf escapes and Damian recovers. Then, Luna wants to explore an abandoned theme park, so she takes Zack, Bud, Geo, and Pat along for the ride. However, strange things begin to occur, and Geo finds himself in a battle with Crown Thunder. However, Omega-Xis notices that Crown is not fused with a living human being, causing his transformation to be impervious.

While Damian and Samantha enjoy their date in the mall, Gemini Spark finally finalizes the transformation between Damien and the FM-ian Wolf, and Wolf Woods rampages through the mall. Mega Man and Lyra Note appear to battle, but ultimately, Samantha is able to calm him down. The FM-ian Wolf escapes and Damian recovers. Then, Luna wants to explore an abandoned theme park, so she takes Zack, Bud, Geo, and Pat along for the ride. However, strange things begin to occur, and Geo finds himself in a battle with Crown Thunder. However, Omega-Xis notices that Crown is not fused with a living human being, causing his transformation to be impervious.

Crown Thunder takes an old pirate ship and prepares to launch it toward Echo Ridge, but Mega Man and Lyra Note battle together to try to stop the enemy. They discover that the pirate ship is the source of his power, and by attacking it, they're able to defeat him. Then, Luna is devastated when she assumes Mega Man and Lyra Note are involved romantically, causing her anger to show at school. Her friends take her to a Sonia Sky concert to cheer her up, but the FM-ian Ophiuchus targets Luna's devastation and offers her the power to capture Mega Man.

Crown Thunder takes an old pirate ship and prepares to launch it toward Echo Ridge, but Mega Man and Lyra Note battle together to try to stop the enemy. They discover that the pirate ship is the source of his power, and by attacking it, they're able to defeat him. Then, Luna is devastated when she assumes Mega Man and Lyra Note are involved romantically, causing her anger to show at school. Her friends take her to a Sonia Sky concert to cheer her up, but the FM-ian Ophiuchus targets Luna's devastation and offers her the power to capture Mega Man.

Geo encounters Ophiuchus Queen, the fusion of Luna and Ophiuchus, who knocks him unconscious. This leaves Sonia to take care of the enemy, transforming into Lyra Note to battle. Mega Man later intervenes, and together, they knock Luna out of the fusion. Ophiuchus escapes. Afterwards, Geo recalls his encounters with the FM-ians from the previous 12 episodes, and he questions the connections between his father's disappearance and Omega-Xis's appearance on Earth.

Tom returns to AMAKEN after weeks of absence, but he is completely under Cygnus's control now. He attempts to throw Aaron off a skyscraper, but Mega Man rescues him. After a heated battle with Cygnus Wing, Tom reveals to Geo that Omega-Xis was the one who killed Kelvin. The startling news causes Geo to collapse into a river where he is washed away.

Tom gathers the FM-ians together and gives them the power to mimic their EM Wave Human forms without the aid of the humans they merged with. Meanwhile, Omega-Xis helps Aaron find Geo's body and he is rushed to a hospital. That night, Geo and Omega-Xis reunite for an emotional argument until Omega-Xis leaves Earth completely.

With Mega Man out of the picture, the FM-ians and EM viruses begin to rampage through Echo Ridge, and only Lyra Note appears to battle. Geo, however, uses his Transer and Battle Cards to try and take out EM viruses, and he notes to his friends that Mega Man will never come back to save them.

When EM viruses threaten to harm Geo, Omega-Xis returns and forces the fusion into Mega Man. Though Geo is angry, they agree to cooperate and battle with all of the FM-ians. However, they are overpowered, and Cygnus Wing captures Omega-Xis for the Andromeda Key. But three forces appear in the sky to stop the fighting, and they take Geo with them when they leave.

Geo meets the three administrators: Pegasus Magic, Leo Kingdom, and Dragon Sky. They explain to Geo what Andromeda is: a machine designed to destroy planets. As Andromeda becomes activated, they offer Geo the power to stop it: Star Force. They help Geo free Omega-Xis from the FM-ians' clutches and, reunited, the two go after the enemies.

Mega Man battles with the FM-ians and uses Star Force forms Ice Pegasus, Fire Leo, and Green Dragon to succeed. Gemini Spark also appears, attempting to steal the Andromeda Key from Cygnus Wing, but an Atomic Blazer attack from Mega Man both destroys Cygnus (freeing Tom) and causes Gemini Spark to flee. Omega-Xis proceeds to smash the key before the two return home, only for Pat to find it in the rubble.

The FM-ians regroup, now without a leader, and try to formulate a plan. However, Cancer has the remains of the Andromeda Key and figures they can refill it with minus energy from the humans. Gemini Spark helps them create a program that can also allow the FM-ians to take on the appearance of the humans they once merged with.

As the FM-ians (in their doppelgänger forms) explore Echo Ridge, Taurus and Wolf decide to transform into Taurus Fire and Wolf Woods to attack the city. Mega Man intervenes, but discovers his enemies can now use Battle Cards. Though the FM-ians have the upper-hand, their power soon drains and they are forced to escape.

Zack continues to try and convince Geo that something is up with Luna and Bud. Omega-Xis eventually realizes that Zack is probably trailing the FM-ians. Sure enough, the two FM-ians attack Zack for following them, but Mega Man intervenes to rescue his friend.

Libra (taking the form of Shepard) starts hosting a popular game show, and Sonia Sky is invited to be a contestant. Meanwhile, the other FM-ians try to find a way to gather minus energy from the game show, but Libra is more interested in hosting it for fun.

The FM-ians attack the game show after Libra neglects to gather minus energy himself, so Mega Man and Lyra Note work together to battle all of them. Libra, upset that his fun is over, turns into Libra Scales and helps Mega Man battle against his teammates.

Wolf, being trailed by Copper, escapes into a young girl's Transer. When he awakes, he finds that he unintentionally entered the body of an EM Wave Pet, now acting as the girl's pet dog. However, he eventually becomes attached to the girl and remains in that form.

Geo enters Omega-Xis in a dog show as an EM Wave Pet as retribution for the telescope set he broke. There, he meets Wolf in the form of a dog, and seeing the full moon causes Wolf to make a startling transformation into Wolf Woods. However, the girl is able to talk him out of it, but Wolf is returning to live as an FM-ian.

While walking through the city, Cancer Bubble witnesses Luna's anger over the possibility that Mega Man and Lyra Note are "dating," and he assumes that her anger is refilling the Andromeda Key. Thus, he follows her through school, attempting to upset her in order to gather energy.

Cancer Bubble and Crown Thunder distract Mega Man and Lyra Note in battle so Cancer Bubble can record Lyra Note's voice and use it to start another conflict with Luna. Soon enough, the two girls are at each other's necks over Mega Man, but find a common ground in beating Cancer Bubble to a pulp.

When Geo breaks his Transer, he goes to AMAKEN to have it fixed, and receives a Wave Scanner as backup. Tom shows him some of his inventions, including a lure for viruses. Unfortunately, the device attracts a large amount of viruses to the lab.

Geo is being overwhelmed by the horde of viruses, and Cancer Bubble makes matters worse by stealing the device and crushing Mega Man with the expanding horde of viruses. Luckily, he accidentally breaks it, and flees rather than fight.

After the game show once hosted by Libra (as Shepard) begins to go under, he begins to drown under the pressure of new decisions. Thus, Libra's mentality is split into two, represented by the elements fire and water. The two fight over control of Libra's body as he seeks new opportunities and overcomes bad luck.

To acquire more fame, Libra (as Shepard) becomes a published author, and everyone is nuts for his book. However, when fame becomes too much, Libra Scales erupts and battles with Mega Man. In order to avoid defeat, the two Libras (fire and water) realize they require each other for Libra's full potential, the two reunite before escaping.

Luna decides to learn how to cook in order to impress Mega Man, and Geo's mother (Hope) offers to give her cooking lessons at the Stelar house. Meanwhile, the FM-ian Ophiuchus (in the form of Luna) has been working constantly in order to feed her fellow FM-ians. Overworked and stressed, she plans to cut her teammates off from her financial income.

Cancer, who finds Ophiuchus's own personal money stash, uses it to purchase an ice-making machine and then proceeds to rampage through Echo Ridge with an artificial ice floe. Mega Man appears and rescues Luna from the wreckage, who was waiting for him to give him some food she prepared for him. When Mega Man later eats it, he's surprised to find it tastes delicious.

A mysterious comet appears close to Earth, and its wavelengths begin to affect the FM-ians in various ways, such as Wolf acting like a house dog, and Omega-Xis becoming exceedingly polite and proper. Against this backdrop Geo is forced to fight Cancer Bubble, who has grown to a prodigious size.

Using the power granted to him by the comet, Crown enters a museum and begins fusing with dinosaur skeletons. Geo happens to be there on a field-trip and fights back as Mega Man. However, since Omega-Xis is still incessantly polite (due to the comet), he becomes uncooperative in battle. Eventually, the comet passes Earth and the effects on the FM-ians subside, marking one more victory for Mega Man.

When Aaron uncovers the space station Kelvin vanished within, Omega-Xis finally tells the story behind his involvement with Kelvin's disappearance on that day. In order to rescue Kelvin and his teammates from an FM-ian attack, Omega-Xis transformed them all into radio waves. Omega-Xis senses Kelvin's presence on the space station, which is broadcasting a Brother Band signal through space. However, the FM-ians suddenly begin attacking Echo Ridge, and Geo rushes to the scene.

Working with Lyra Note, Mega Man battles the FM-ians as they attack Echo Ridge. Amidst the battle, the Andromeda Key is broken, and all of the gathered minus energy is lost. Then, the FM-ians' king sends a signal to his soldiers telling them to withdraw from their attacks on Earth. Aaron suspects that Kelvin used Brother Band to convince the FM Planet that Earth is not hostile. However, Pat is not content with withdrawing from Earth, so as Gemini Spark, he murders Taurus one night and harnesses his body as energy for a new Andromeda Key.

Gemini Spark's spree continues as he systematically deletes his former comrades to fill up the Andromeda Key, forcing their wave forms out of their W bodies and brutally murdering them one by one. Geo, meanwhile, receives the Star Carrier from Tom, and Omega-Xis encounters Cancer—the only survivor of Gemini's rampage—pleading for help.

Gemini Spark go after Sonia in an attempt to delete Lyra, but Geo intervenes to rescue her. In the process of defeating Gemini Spark, Pat's identity is revealed, and Sonia also learns that Geo is Mega Man. With all the secrets out in the open, Geo and Sonia agree to fight together for Earth's safety. Meanwhile, Gemini Spark uses the gathered energy to revive Andromeda.

Revived, Andromeda proceeds toward Echo Ridge, annihilating cities in its path. Mega Man and Lyra Note attempt to stop it but are overpowered. Lyra Note is left incapacitated, so Mega Man proceeds alone with Star Force, but his attempts are in vain. Amidst the battle, Luna, Bud, and Zack witness Mega Man revert into Geo (Luna was only half-conscious at the time, and this shows in later episodes, where she says that it's impossible that Geo was Mega Man).

The Satellite Administrators sacrifice themselves in order to destroy Andromeda. However, Gemini Spark White murders his other half to harness his minus energy and revive Andromeda once more, but Omega-Xis is able to crush the key before the Earth is erased. Afterwards, the FM-ians' king Cepheus descends onto Earth to take responsibility for his wrongful attacks on Earth, defeating Gemini White Spark personally. He also grants Geo the chance to speak with his father, although his father is not yet ready to return home. Pat's body is also discovered, with no memories of meeting Gemini and after. With the war against the FM-ians over, life is a lot brighter for Geo and his friends.