- Wily's factory password is "OLGA," the name of his talking AI in the Mega Man Fan Film.
- One to Linkara's "I AM A MAN!" punch occurs in chapter 22, and became a running gag.
- The Mega Man Robot Masters decide to challenge Mega to Mortal Kombat. Though they mean actual fighting, the word's spelled with a K, like the game franchise.
- The Mega Man 2 Robot Masters' personalities are based off the character classes from Team Fortress 2.
- The Mega Man 3 robots' personalities are based off of Street Fighter and Metal Gear. Magnet Man's is a mix of M. Bison and Magneto.
- Some to fellow fic Mega Man: Defender of the Human Race have shown up, like Megaman being called as such and rescuing a Metool from one of Wily's areas.
- Wood Man calls Mega a Cossack entering a citadel. In Mega Man 4, Dr. Cossack's castle is called a citadel.
- The Arc 3 finale has one to Ruby-Spears' Mega Man cartoon by mentioning Wily's holographic projector looks like a smaller one that the show used.
- Higsby mentions taking inspiration from anime when designing robots, much like Otacon from Metal Gear Solid.
- Arc 4, chapter 2's secondary title is a shout out to the Bill & Ted films.
- The Neo Emerald Spears, who are based off the Emerald Spears from Archie Comics' Mega Man, appear in Arc 4.
- Robert talking down a suicidal man is one to All-Star Superman, where Superman does the same to a teenaged girl.
- Robert reading his deceased father's journal, which has a letter to him, is one to DC's Flashpoint series where Bruce reads a letter from his father.
- Arc 5, chapter 1 has "It's a secret to everybody."
- Top Man's chapter is a Whole Plot Reference to Jet Set Radio.
- Shadow Man's personality is a reference to the Cyborg Ninja/Grey Fox from Metal Gear Solid.
- Snake Man has a hiss, like his Ruby-Spears counterpart.
- Gemini Man's coin flips and split personality are a shout-out to Two-Face/Harvey Dent from Batman.
- Needle Man's chapter has several references to Sonic the Hedgehog.
- Robert jokes about the Teenage Mutant Ninja Turtles when fighting the Kerogomo turtle robots.
Shout Out / Mega Man Reawakened