Rock and Roll escaping from Skull Fortress after Wily reprograms the Robot Masters and captures them. Unlike in the show, Wily and ProtoMan don't fall for Rock's lie about the warrior robots, so they have to fight their way out.
Episode 1 has Mega Man volunteering to defend the human race from Dr. Wily.
Mega Man gets one in Episode 2 for infiltrating Skull Fortress and nearly stopping Wily right there.
Episode 3 has Doc sacrificing himself to save Roll.
In Episode 3, Mega talks Roll down from chasing Wily after Doc's death.
After Gamma shoots Mega and Rush down in Episode 4, Roll rescues them both and takes them to where they can be repaired.
Roll defeats several Robot Masters during the series, and was instrumental in helping Mega stop Gamma.
Lynn got one for helping her brother Castor against all odds.
The climax of Episode 5 has Mega and Proto saving each other's lives, even after ProtoMan's betrayal.
In Episode 6, Kalinka has a heart-to-heart with ProtoMan and questions why he does what he does, causing him to think it over.
Mr. Black, a human with no special powers aside from gadgets, fatally shoots Dark Man in Episode 6.
In Episode 7, Mega got one for only accepting Vick-Tek's challenge to fight Bass if it was for charity.
The Vick-Tek board members get one in Episode 7 for giving an unanimous vote of no confidence in Vickers, effectively ousting him from power.
Dr. Light gets one in Episode 7 for chewing out Vickers about what happened because of his greed.
In Episode 7, a Met that ProtoMan rescued from Wily testing a painful device on singlehandedly takes out Skull Fortress' security system.
Bass gets one in Episode 7 for defeating Mega Man singlehandedly; he would've won if not for ProtoMan's assistance.
ProtoMan framing Bass in Episode 7, as well as reprogramming Toby the Robot Warrior to be useful.
In Episode 8, the female robot master, upon being activated, demolishes a path out of Skull Fortress and even evades ProtoMan.
In Episode 8 Brain Bot is able to successfully analyze the material Bass is made of, and assists in the construction of a gun that almost works at getting Mega Man into the tower.
The climax of Episode 8, with Roll managing to talk Drill Man out of obeying Wily's orders and drilling into the core of the Earth by reminding him of his basic programming; it states robots can't self-terminate at the behest of a human. This fact was established way back in Chapter 1.
Drill Man himself gets one for listening to Roll and defying Wily.
ProtoMan's plan in Episode 9 to capture Galaxy Man works perfectly, and the Robot Masters even defeat Mega Man.
Proto also has a good showing against Bass by nature of being unpredictable, and when it's apparent he's going to lose, the other Robot Masters and police watching the fight scare Bass off.
ProtoMan's plan in Episode 9 after Galaxy Man is captured. If Wily hadn't bragged about it to Mega and tried to alter it, it's likely he and Roll wouldn't have known its scale at all—and there are things Wily didn't reveal to Mega.
Episode 9's initial battle with Galaxy Man has Mega pulling out all the stops to save his family, even at the expense of his own energy.
Mega Man stopping Galaxy Man in Episode 9 by using an idea ProtoMan had tried.
In the same chapter, Roll uses her plumber's snake to snag Wily and nearly captures him.
As dark as it was, and despite the ramifications, ProtoMan killing Metal Man was intensely awesome, especially as the latter faced death with dignity and had many moments that made readers hate him.
Episode 10 has the three Mega Man Killers soundly defeating many more Robot Masters.
In Episode 10, the Mega Man Killers have defeated Mega Man, and are prepared to finish him off. As they argue over who gets to finish him off, a rocket launcher from Police Chief Toombs and assistance from other officers knocks them back and forces Wily to retreat.
Ballade gets one when Mega Man tries to copy his weapon; corrupted data is transferred and his weapon is safe.
Episode 10 reveals that when ProtoMan was training the Mega Man Killers he studied them to learn their weaknesses, and he didn't teach them everything.
Yet another from Episode 10, as Mega Man distracts the Killers by targeting Wily. Roll and Rush hold their own in combat, with Roll even threatening Wily personally, and both sides regain the advantage in pretty cool ways. And Punk has reason to take Roll as a serious opponent.
Then Bass shows up unexpectedly and proves just how strong he is by thrashing the robots that just defeated Mega Man.
At the same time, Mr. Black successfully invades the Light household, tasers Beat, and absconds with Light's files—one of which contains vital data on Mega Man. Bonus points to the author for making that last twist so unexpected, as it happened a mere 2 chapters after Mr. Black gained access to the lab and was in the middle of a huge fight.
In Episode 10, Mr. Black manages to blackmail the Conduit, who'd previously been tormenting him with threats to fire him.
Mega Man's no-nonsense way of dealing with the Robot Masters and Killers as they threaten the girl he loves.
Even after a direct order from Wily during an interrogation, ProtoMan refuses to sell Nomad out and avoids mentioning her.
Bass saving Roll from a collapsing building in Episode 11, chapter 5.
Episode 11. Chapter 8. ProtoMan finds the strength to redownload his courage and confidence, and he is angry about what Wily did to him.
Episode 11, chapter 9, has Roll literally slapping some sense into Mega Man after he tries to quit fighting Wily. Then he reviews the footage and memories of all of Wily's prior attacks so he has a clearer mindset of what he's fighting against... and the humans he's fighting for.
ProtoMan's full He's Back moment to Wily, Bass, and the Robot Masters.
Episode 11, chapter 10, has President Keith Henry's defiance of Wily and determination to stall him until Mega Man can arrive.
It also has ProtoMan pretending to act scared so he can get the drop on Punk. Then Proto soundly defeats him.
Bass makes extensive use of his advanced scanners throughout the chapter; he's able to tell when the President's heart rate is elevated as well as scan through walls and floors.
Episode 11, chapter 11, has Mega Man decisively defeating Bass and Treble, complete with amazing fight scenes and taunting Bass for once.
It also has a villainous one with the reveal of just how strong the Mad Grinder is; even after soundly defeating Bass, Mega Man was nearly killed by the war machine.
Finally, it has the awesome moment. ProtoMan, even after a direct order from Wily and a reinstilled fear program, turns on the doctor to save Mega Man—and takes out the Grinder via overload. By doing that, he saved his brother and the world.
Episode 11, chapter 12. To cement his character development, ProtoMan literally gives Mega Man his heart to help save him.
Miss T gets a villainous one in Episode 12, chapter 2, when she successfully invades Mr. Black's hideout and finds what he had been hiding.
Mr. Black gets one as well in the same sequence for being able to escape her.
The chase between the heroes and Mr. Black in Episode 12, with Mega Man, Roll, and ProtoMan working as a team to catch him.
The interrogation of Mr. Black is one for Mr. Black, as he manipulates Mega Man into doing what he wants.
Episode 12 has the fight between the Conduit's forces and Wily's forces, as well as Mr. Black nearly getting his revenge before Bass intervenes.
The Episode 12 epilogue has Tiesel telling the Conduit that it was his own fault the plan failed, showing he has character even in a terrible situation.
The Episode 12 epilogue has Mr. Black letting go of his hatred, accepting the loss of Tonya, and using his knowledge to help people, starting with Janet.
Splash Woman gets evilly awesome moments when she interrogates Plum and pushes her into the ocean, and later captures Mega Man and Rush.
Splash Woman successfully uses her powers on Bass and Treble... or so it seems. They were faking it to see how far she'd go in using her powers.
Bass is so determined to keep Roll safe he tells her Splash Woman's entire plan and how to stop her brainwashing frequency.
Kalinka volunteers to help save Mega Man and Rush from Splash Woman, putting her robotics skills to good use.
Burner Man has an impressive debut, where he opens a safe that none of the other Robot Masters could get into.
Roll bonks Splash Woman on the head with her frying pan with enough force to crack her helmet when Kalinka is threatened.
Bass's plan to pin the failure of the Hawaii operation entirely on Splash Woman.
Tron Bonne saves Roll from a plasma blast with her harpoon gun in Episode 13, letting Roll finish Splash Woman off.
ProtoMan takes on an entire group of Robot Masters in Episode 13 and wins.
Even though the US Military loses the battle with Wily in Episode 13, they put up a very good fight.
Bass expertly lies to Wily about Splash Woman's failure and says she was destroyed—and when she tries to protest, he threatens to really scrap her if she doesn't back off.
In the Episode 14 interlude, Bass has his brain hijacked by the Stardroids, giving them access to his memories and knowledge of Earth so they can prepare for the invasion. Even scarier is that they did so through his power source, and someone who wasn't the Stardroids actually possessed him briefly, sending out a signal to call the Stardroids to Earth.
When the Stardroids arrive, Terra hacks every electronic device in the world to broadcast a message demanding Earth surrender. They kicked off the invasion by effortlessly dispatching Galaxy Man, who had been trying to have peaceful contact with them.
The Stardroids' first battle is a complete rout; they toy with the humans and robots trying to stop them, showing off their weapons and disregard for life as they do. Only Pluto receives minor damage, and Terra takes no damage at all from the heroes. Bass is able to damage them more fully, but even he is forced to retreat.
The Prime Minister of England is successfully hidden away when the Stardroids demand he surrender, and the Queen of England calls them out and also refuses to surrender.
Duo's entrance on Earth is a major source of hope for both the heroes and the readers, as he promises to help Mega Man and his family fight the Stardroids.
The flashback to Duo's great battle with the Stardroids. Both sides get awesome moments throughout, and it ends with Duo punching Sunstar and Luna to pieces. However, Terra and Sunstar enacted a plan to allow their race to survive.
Thanks to the new weapons Brain Bot developed, Mega Man and his team are able to hold their own against the StarDroids when they meet in Dallas.
Bass takes on seven StarDroids at once in the climactic battle and comes out on top, mainly due to the Robot Master weapons installed.
Mega Man, Roll, ProtoMan, and Duo all team up to take down Luna and Sunstar for good.
Neptune turns on his fellow StarDroids to aid Duo and Mega Man, dying with honor.
The Episode 14 epilogue ends with Wily finally testing the Jadous Sphere shard. It makes a tiny laser so powerful it blows a hole through several walls of the entire fortress, enough to barely see outside.