Aki saves Silicon City as Mega Man along with his miniature sidekick Mega-Mini. Only his human sister, Suna, knows of his double identity. Their father, Dr. Thomas Light, arrives at school to give a lecture on human and robot relations, but are interrupted by Sgt. Breaker Night who considers robots inferior. Fire Man appears and begins to attack Sgt. Night and Dr. Light and Aki transforms to fight him, but during the scuffle is knocked away.
Mega Man manages to replicate Fire Man's schematics, but he also replicates his anger, making him unfocused. Sgt. Night tries to push his point forward while Dr. Light and Suna try to help the students. Mega Man returns to battle Fire Man and overcomes his anger with the help of the students and robots who band together. Fire Man escapes and returns to his boss who turns out to be Sgt. Night who now plans on defeating Mega Man in order to control Silicon City.
At school, Aki struggles with the side effects of his newly replicated Drill Man schematics; later, as Mega Man, he learns to control his Fire Powers in thwarting Drill Man's assault on Skyraisers Inc.
Mega Man must stop Hypno Woman from turning the students and teachers at Silicon Central into her mindless drones.
A misunderstanding between Mega Man and Rush ends in the robo-pup running away from home, only to be reunited and reconciled during a confrontation with Wave Man.
Mega Man and Suna must overcome a sibling dispute over what to do on their day off in order to stop Fire Man from overheating the city.
An "unscheduled" TV appearance not only lands Aki in hot water for missing class, but sets Ice Man on a misguided mission to "unite" (i.e. freeze together) every human and robot couple in the city!
Mega Man must stop Blasto Woman from plundering the Museum of the Hard Age and its cache of military grade weaponry.
Mega Man tries to save Dr. Light from a date with "Mari," who's actually Hypno Woman in disguise!
Student elections get blown out of proportion (literally) when Air Man lends his support to Aki's rival for class president, Peter Punk.
Aki must set aside a petty rivalry with Bert Wily in order to stop Chemistry Man from wreaking havoc at Silicon Central's Field Day.
Fire Man and Wave Man team up to evaporate the city's water supply, forcing Mega Man to team up with an ally of his own-Suna.
When Ice Man decides to be a hero, Mega Man, influenced by Ice Man's literalness, steps down from the hero biz until a true crisis snaps him out of it.
Guts Man tries to undo Dr. Light's eco-friendly disposal of trash in Silicon City by infiltrating the family and destroying the Lighthouse so he can eat it!
Mega Man tries a quick fix using Hypno Woman's powers to rehabilitate Drill Man, to disastrous results!
After replicating Elec Man's powers, an underslept/overcharged Mega Man goes on a 24/7 hero spree that ends up turning him into his own worst enemy.
Mega Man teams up with his crush, Ashley Adderley, to solve a series of science riddles left by Chemical Man, who's plotting to turn all the city's metal into rubber.
Mega Man accidentally awakens Wood Man, who thinks it's still the Hard Age, and sets off on a path of destruction toward Silicon City.
The mysterious Lord Obsidian calls Mega Man a traitor to robots and challenges him to a duel. An overconfident Mega Man is humbled by this mysterious new villain.
Lord Obsidian attacks the Lighthouse, but Mega Man overcomes his insecurity and works with his family to repel the big bad, who's rescued at the last second by a mysterious lieutenant, Namagem.
Rush puts his new battle upgrades to the test in a battle with Wave Man.
Namagem attacks Mega Man using a variety of powers, revealing that they both can replicate schematics, although Namagem can carry more than three at a time.
When Mega Mini is kidnapped by Blasto Woman, Mega Man must track down his missing partner without the full use of his own systems.
Aki and Bert accidentally damage a bonsai tree outside the Lighthouse, sending the Lights' perfectionist gardener on a slicing-and-dicing spree as Cut Man.
Mega Man gives out the Mega Man Emergency Code to the public, but it results in him doing low-stakes house calls that he feels are beneath him. He suddenly gets a contact from Hypno Woman who has him come to the power plant where she has hypnotized the workers to shut down the city. Despite Mega Man warning her of an overload, she continues with her plan. Suna gets Rush to give Mega Man his Hypno Woman schematic and the two of them (who are immune to Hypno Woman's powers) team up and defeat her. Mega Man realizes that it is important to care about the minute details and he happily returns to his calls.
While on his way to school to meet with Ashley about a drone project, Aki transforms into Mega Man when the city is apparently under attack. He ends up meeting Man Man, a clumsy DIY superhero and they trace Guts Man to the school where he intends to complete his task of eating ingredients to make himself stronger. Mega Man is upset with Man Man's interference, but a sudden unintended blunder on Man Man's part allows the two of them to defeat Guts Man with the two reconciling. Mega Man makes it to class on time and he uses Man Man's gum technique to fix the drone which earns him and Ashley an A+.
Mega Man must stop Namagem and an army of hypnotized Good Guild bots from breaking into Dr. Light’s lab.
Air Man stakes a claim on the skies above Silicon City, threatening anything that trespasses on his airspace.
When Elec Man derails the school play by hijacking Silicon Central's power, Aki/Mega Man must use what he learned onstage to defeat his supercharged foe.
Aki and Suna take a rehabilitated Ice Man out for a day in the city, but things take a turn for the worse as he misinterprets their cues and turns a game of hover hockey into a literal freeze out!
When Namagem starts using his Hypno powers to haunt Aki's dreams, our hero must face his fears in the dreamscape.
Mega Man teams up with Bert Wily to take down Drill Man, whose plan to construct hundreds of drill shaped high rises has put Silicon City in both aesthetic and physical danger!
Suna and Ashley work on their science project. It turns into a blob monster that eats anything. When Silicon City is threatened by the blob monster, Mega Man must team up with Wood Man to defeat the blob monster.
While on a hiking trip, Aki loses Ashley's camera and heads out to retrieve it. He soon stumbles on a plot by Fire Man to supercharge his blasters with lava from a dormant volcano with the help of Sgt. Night's Blaze Enhancers. When Fire Man starts to destabilize the volcano against Sgt. Night's orders, Mega Man and Fire Man must work together to stop the volcanic eruption.
Aki needs a new hairstyle for school picture day and finds that Cut Man has started working as a hairstylist much to Sgt. Night's annoyance. To do his own hair, Mega Man copies Cut Man's schematics which sends him on a minor perfection spree throughout Silicon City. This puts him in a competition with Cut Man who, after accidentally messing up Bert's hair, has a mental breakdown and starts messing up Silicon City.
Aki has been stressed from all the crime-fighting he has been doing. A prankster robot named Chaotique is causing mischievous trouble in Silicon City. She then persuades Mega Man to take a break from his crime-fighting as he and Bert join her in some harmless pranks. When Chaotique frames Bert where he is apprehended by the Good Guild, Mega Man must defeat Chaotique and clear Bert's name.
Guts Man has been outdoing Mega Man in a strength battle as he goes on a consuming spree. This forces Mega Man to copy Guts Man's schematics where he discovers that he not only has his super-strength, but also his insatiable appetite for human food. Meanwhile, Lord Obsidian establishes a wall as he has Guts Man, Air Man, Drill Man, and Elec Man separate the humans from the robots' side of Silicon City.
Mega Man is lured to the bank where Blasto Woman has an offer for him. In order to prevent a powerful EMP emitter from falling into the wrong hands, Mega Man works together with Blasto Woman to stop the heist. At the advice of Suna, Mega Man prepares a Plan B just in case of a double-cross....especially when Blasto Woman plans to disable Mega Man and sell him to Lord Obsidian.
Mega Man has started to become envious at the fact that Namagen can wield four abilities at a time. This causes Mega Man to have Mega Mini remove the safeguard so that he can use his schematics. However, he starts suffering from debilitating mood swings from each of the schematics. Lord Obsidian's claims to Mega Man and that he can answer the questions that Dr. Light knows and holds a challenge against Namagen. Mega Man's overload causes Suna and Rush to come to his aid.
Mega Man undergoes Suna's training to deal with the personality glitches. A bunch of tornadoes have been causing destruction in Silicon City ruining one of the takes of movie director Mary Flair, destroying the generator for the renewal energy turbines of inventor engineer Volt Aire, and sabotaging the test run of stunt pilot Captain Dare. It is eventually revealed to Mega Man and Suna that the three are siblings with Air Man, who was always put down by his siblings and developed high insecurity which he hid with his arrogant attitude.
After learning that his replacement Mrs. CHO was presented with a teaching award, Chemistry Man lays siege to Silicon Central.
A rare and noxious flower called the Corpse Flower is stinking up Silicon City. Unfortunately, Wood Man won't have any harm come to it. Mega Man must go up against Wood Man to decide the fate of it the Corpse Flower.
There is a grudge match in Silicon City between Fire Man and Namagen. As this grudge match is threatening Silicon City enough to cause collateral damage, Mega Man must pick a side and put an end to it.
Chaotique is planning to erase Silicon City at a subatomic level. While learning some life-lessons from a rambling elderly robot named Hal, Mega Man must work to keep Silicon Central from being erased.
Drill Man wants revenge on his overbearing father. Meanwhile, Aki and Dr. Light have a father-son disagreement. The two of them must put aside this disagreement in order to defeat Drill Man.
When a run-in with the Hoover Gang leaves Aki unable to transform into Mega Man, he must don a cheap costume and enlist the unlikeliest of sidekicks, Man Man!
Mega Man tries to stop Elec Man by helping him overcome his destructive habits, but is he being duped in the process?
Desperate for answers about Namagem, Mega Man decides to break into his father's lab, which leaves Suna exposed to the vengeful robot.
Mega Man goes on a 24/7 heroing spree around the city, forcing Suna, Bert, Ashley, and Rush to deal with the problem at hand, Cut Man.
When Chaotique breaks into Dr Light's Lab Mega Man must shut down his frenemy and the lab's defenses before either of them get destroyed.
Lord Obsidian unites the Robot Masters against Mega Man and his family for an epic showdown at the Lighthouse.
As Dr Light and Suna turn the Robot Masters against each other, Mega Man defeats and unmasks his archnemesis, Lord Obsidian.
