This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Mega Man Reawakened
Robert's unstoppable rage modes. He goes berserk on his opponents with little care to them or himself, and often has to be snapped out of them.
Related to those is his dark side, which manifests as an evil version of Robert late in Arc 3.
The reveal that Dr. Wily rigged the explosion that killed Robert's father, and was intending for it to kill Dr. Light.
Top Man's bombs threaten to wipe out an entire city.
Shadow Man's chapter has Robert walking through a corridor of split oil and blood.
Bass's creepiness towards Roll in Arc 5, chapter 5.
Spark Man threatens to detonate and take out an area of 30 miles.
While funny, when Tron is snapping at Robert for something related to a past chapter, it seems that without him she'll lose it...
Snake Man poisoning Robert in Arc 5, chapter 6. It nearly kills him.
Gemini Man's split personality even scares Robert. When his murderous side first emerges, it's especially scary.
Gemini Man: Oh, don't you fret. We knew you'd come by. Because after all... We want in on the massacre!
Needle Man tries to finish Robert off with a bomb after he's defeated.
As of Needle Man's chapter, Robert's dark side may be returning.
Doc Robot Wood Man encourages Robert to use his hatred again.
Robert and Roll arrive to the last Doc Robot area and find it deserted, with the enemies brutally destroyed. They soon find out that Break Man did it, but he'd already left by the time they got there. When he calls Robert up to tell him where to meet him, Bass overhears this and goes there to try and kill him.
Darian Darhk intercepts Wily as he goes to steal Gamma and holds him at gunpoint. Wily is unfazed by this and overpowers him, continuing what he was doing.
Bass pays Break Man back for defeating him and gets ready to kill him despite orders to bring him in alive, saying he'll tell Wily that he died fighting his own brother.
Dr. Wily's ultimate plan for Gamma is to equip it with nuclear weapons.
The Yellow Devil Mark II nearly kills both Mega Man and Rush by holding them down in its gel and crushing them with a mace.
Robert and Bass's Mutual Kill late in Arc 5, which brings both to the brink of death.
During an argument with Bass, Wily threatens to shut him down with a remote.
Wily had a mole in place at Light Labs to help him steal Gamma, and it's revealed to be General Yancey.
Wily's ranting when he activates Gamma even scares Robert.
"Hear this! Your blood will be the first to be spilled by my glorious new weapon! Consider it an honor... a gift from your friend. Now, I will show you! I will show them all the power that once led humanity in the 21st century!"
After Shadow Man is killed, Robert's rage takes over so strongly that Tron senses it back at the lab, and his armor and eyes change color. He even makes Top Spin scary, as he's going so fast he can't be stopped.
After Gamma is disabled, Robert tries to kill Wily and is stopped only by the ceiling falling on them both.