* Episode 1 has the scene where Dr. Wily kidnaps Rock and Roll and nearly kills Dr. Light. It's drawn out, and he shows each Robot Master's power to terrifying effect.
* The scene where Wily nearly reprograms Rock and Roll is also scary, as unlike in the show, he and [=ProtoMan=] don't fall for Mega's lie about the warrior robots. He also describes the reprogramming process in detail.
* The voices in Wily's head, which drive the doctor to do ''very'' evil deeds.
* Wily kills Doc himself with the guns on the Skullker, and he was aiming at Roll to begin with.
* Wily forces Governor Cochran to step down by threatening to have Pharaoh Man burn Cochran's wife's face off.
* In the adaptation of "Electric Nightmare," after Wily makes the cosmetic robot capture and humiliate Roll with makeup, he tries to have her ''kill'' Roll with a buzz saw.
* Roll brutally dispatches the cosmetic robot from "Electric Nightmare" by cutting her in half and vacuuming her face off. Once she calms down, she's frightened of herself and what she'd become.
* Gamma and its Wily-made successor, Project G-2, due to their sheer power and the scope of the battles with them. Both nearly kill Mega Man several times, and the results of both battles change the world.
* Gamma is the first opponent to decisively defeat Mega Man; its laser blows his arm off when he tries to shoot at it.
* Mr. Black, a human with no special powers aside from gadgets, fatally shoots Dark Man in Episode 6. Making this worse is that he could have hit and killed Mega Man, as the two were locked in combat at the time and Dark Man had assumed Mega's form.
* Bass and how powerful he is left some readers ''very'' worried about their favorite characters. The author has stated he's the most powerful robot in the series thus far, and it shows.
* Mega and company coming ''this close'' to death via Galaxy Man's Black Hole Bomb three times in the span of two chapters.
* In Episode 9, [[spoiler:Metal Man]] is ''vaporized'' by the Black Hole Bomb, and the same fate almost befalls the heroes.
* [=ProtoMan=] having his plasma generator torn out of his arm from the Black Hole Bomb's suction.
* Like Bass, the presence of the Mega Man Killers is quite frightening; they've been shown to defeat a lot of Robot Masters and have severely injured both human and robot police. In their first confrontation with Mega, the only reason they ''don't'' kill him is due to in-fighting over who finishes him off.
** Later on, Bass and the Killers fought. Bass won easily, which left readers and characters even more terrified.
* Mr. Black invading Dr. Light's lab, tasering Beat, scaring Kalinka and Peekaboo, and hitting Light so hard he nearly breaks a rib.
* During Episode 10, Wily uses his rage to construct a sketch of a new robot heavily implied to be [[spoiler:Zero]]. He continues work on it in all subsequent episodes, using the ''mention'' of such a powerful force to keep Bass in line.
* [[spoiler:[=ProtoMan=]'s torture]] in the Episode 10 epilogue. Wily describes it in excruciating detail.
* Episode 11 has Project G-2 [[spoiler: slaughtering the entire army sent to fight with Mega Man]].
* Mr. Black's memories of Wily's first attack in Episode 11. [[spoiler: His wife, Tonya, dies, and rubble from the ceiling ''broke his spine'']]. He also saw policeman Ash Rose's brother die in front of him.
* In Episode 11 Wily storms the White House, and demands at one point that the President order a nuclear strike. In the following chapter, [[spoiler:the Mad Grinder]] nearly kills Mega Man, and ''would'' have if not for [[spoiler:[=ProtoMan=]]]. Then there was Wily's order for [[spoiler:[=ProtoMan=]]] to do the deed.
* Dr. Wily has come ''extremely'' close to winning the world and killing Mega Man at times. The most prominent example is Episode 11, where he ''would'' have won and killed him if not for [[spoiler:[=ProtoMan=] turning on him]]. Even after Wily loses in that episode, Mega Man almost dies anyway because of the wounds inflicted on him.
* The extent of Mega Man's injuries in Episode 11, chapter 12. Dr. Light had to soak up Mega's oil with his lab coat. If he were human, oil would be ''blood''.
* The interlude to Episode 12 has [[spoiler: the Conduit's associates planning to take out Mr. Black]] and Wily [[spoiler:planning to take [=ProtoMan=] back from Dr. Light, as well as considering installing a brainwashing program in his latest creation]].
* Episode 12, chapter 2 has the reveal of the Conduit's plan. [[spoiler:It's to spread a virus that destroys robots' memory cores, with the intention of committing genocide against them]].
* The Conduit casually mentioning that there are ''two'' Jadous Spheres.
* Mr. Black [[spoiler:knows ''everything'' about Mega Man and Kalinka]], and uses that information to force Mega's hand.
* The climax of Episode 12 has [[spoiler:the fight between Wily's forces and the Conduit's forces]], Mega Man and [=ProtoMan=] in danger of being killed, Bass claims the Jadous Sphere shard, and ''especially'' the final fight of the chapter, where [[spoiler:Mr. Black nearly kills Wily... but Bass stops him, brutalizes him, and leaves him with a broken neck]].
* The Episode 12 epilogue has Miss T being willing to kill Tiesel and Mr. Wire--though the Conduit threatens to kill ''her'' if she messes up again.
** In the same chapter, Wily and Bass briefly argue over who will use the Jadous Sphere shard.
* The Conduit has a mole in the police force and possibly the FBI. It's later revealed to be [[spoiler:Captain Tallarico, AKA Miss T]].
* In Episode 13, the Conduit and Miss T call Tiesel up, threaten and bribe him, and say that if all goes to plan the war will be over by November.
** In the same chapter, Dr. Wily decides to use the Jadous Sphere shard.
* Splash Woman's brainwashing powers. She seduces Mega Man to the degree that even thinking about Kalinka can't ward off her control. Later, she brainwashes Plum and uses her to spy on Mega Man and his family.
* After interrogating Plum, Splash Woman pushes her off the rocks and into the ocean, where she sinks to the bottom. The narration notes that even if she lives, she's too weak to swim to the surface and it's unlikely someone will find her.
* In Episode 13, Splash Woman captures Mega Man and toys with him before revealing he's strapped to something called a Torment Generator. The following chapter reveals that the Generator is an electric torture device, and Bass exploits this for an interrogation.
* Episode 13 reveals that Nomad will [[spoiler:try to kill Mega Man on sight]] due to Wily's programming.
* In Episode 13, after Bass fails to torture Roll's communication number out of Mega Man, Splash Woman brainwashes Mega Man and successfully gets him to talk.
* Splash Woman uses her powers on Bass and Treble and successfully seduces them...or so it seems. They were faking it, which means they can ''resist'' the brainwashing powers that almost completely controlled Mega Man.
* Episode 13 has a fake-out where it appears Plum is dead when her body is recovered from the ocean. She revives a few paragraphs later thanks to intravenous energy transmission, but it's a very tense scene even after she wakes up.
* In Episode 13 Splash Woman tries to brainwash Roll, and her performance is so convincing that Kalinka worries she ''has'' been brainwashed.
* In the final battle of episode 13, Splash Woman almost fries Kalinka with her trident, and Dark Man 2 poses as Roll to deceive Kalinka.
* The Episode 13 epilogue reveals the mole within the police department... and they were put in charge as the Police Chief after Toombs was falsely arrested. It's [[spoiler:Captain Tallarico, AKA Miss T]].
* 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.
** Splash Woman also goes on a scary rant about what she'll do to Roll for defeating her, saying she'll tear her apart and wear her ponytail as a trophy.
* For a more realistic scare, in the interlude to Episode 14, [[spoiler:Tiesel Bonne gives footage of Mega and Kalinka's kiss to the Conduit]], opening Mega Man and Kalinka up to tabloid scrutiny like never before should the footage be leaked.
* 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 [[spoiler:someone who wasn't the Stardroids]] actually possessed him briefly, sending out a signal to call the Stardroids to Earth.
* Episode 14 features the Stardroids, some of the most powerful classic series antagonists. Terra is the only being to defeat Mega Man in-game, and [[spoiler: Sunstar has ''no weaknesses'' and three forms]].
* The beginning of Episode 14 has Tron planning to scare Kalinka into giving Mega Man up by knocking on her doorstep with the Gustaff mech.
* The first chapter of Episode 14 ends on a very ominous note as Bass has his brain hijacked again, and calls the Stardroid Terra by name when he had never met him before.
* 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.
* Wily and the Stardroids form an uneasy alliance in Episode 14, with each party planning to backstab the other at their earliest convenience.
* Duo's sensors indicate Dr. Wily is ''the most evil being alive on Earth''.
* A funny scene with Tron giving her brother a computer virus turns scary when [[spoiler:he decides to use it as a template for the Conduit's virus]].
* Duo's flashback to his battle with the Stardroids shows just how terrifying and ruthless they are. [[spoiler:Their greatest weapon, Luna, is a planet devastator that exterminates all life on planets by freezing their cores, allowing the Stardroids to reproduce before blowing the planet up. Their leader, Sunstar, has no qualms with allowing some of them to be destroyed so long as they stall Duo, and he lies that they are the last Stardroids to get them to give their all.]] The crossing of the MoralEventHorizon came when they destroyed the planet in front of Duo's eyes. Then there's their contingency plan, which resulted in Terra and his group finding Earth years later.
** The Stardroid Beta screams for help as Duo attacks her, and Terra deliberately misses so as to not help her ''too'' much.
* The Stardroids' plan hinges on reviving Sunstar and Luna from the dead. [[spoiler:They succeed with Sunstar in chapter 153]].