* 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.
* 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.
* [[spoiler: Bass]] and how powerful he is left some readers ''very'' worried about their favorite characters.
* Mega and company coming ''this close'' to death via Galaxy Man's Black Hole Bomb three times in the span of two chapters.
** [=ProtoMan=] having his plasma generator torn out of his arm from the suction.
* Like [[spoiler: Bass]], the presence of [[spoiler: 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, [[spoiler: Bass and the Killers]] fought. [[spoiler: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.
* [[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.
* 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, [[spoiler:Bass powering himself up with a 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, [[spoiler: 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.
* In Episode 13, chapter 1, 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.
** The same chapter has Wily [[spoiler:deciding 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 [[spoiler:pushes her off the rocks and into the ocean, where she sinks to the bottom]]. The narration notes that [[spoiler: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 [[spoiler: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, [[spoiler: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 [[spoiler:Bass and Treble]] and successfully seduces them. [[spoiler: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 [[spoiler: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.