* In Act 1 Megaman is missing his iconic PowerCopying ability, or so it seems. During all of act 1 the only named robot he defeats is [[spoiler: Protoman]], after which he adopts the same view point [[spoiler: and forsakes mankind just like Protoman did.]] Copying his views, not his powers.
* Why does the HeartbeatSoundtrack start as the same time as the synths in Act II? [[spoiler: Because it's when Joe's born!]]
* In the games, the Sniper Joe robot was based on Protoman. The Sniper robot explains how Light got materials to make Protoman in Act I.
* In "Funeral For a Son", why were the people whispering of Protoman? [[spoiler: Because he was alive, working for Wily, and oppressing them!]]
** Also: [[spoiler: [[HeWhoFightsMonsters He fought the darkness]], [[FaceHeelTurn the darkness won.]]]]
* Why did Light build Protoman to fight rather than building some sort of armour for himself or another human? Act II explains that he builds robots to 'take the death away' from jobs.
** He DID use another human at first. It didn't end well. It parallels his and Wily's initial goal to replace human miners with robot ones.
* Remember Light and Wily's argument back in The Good Doctor? Most people assume that it was Wily who ultimately won the argument, as the entire first album shows. But that's not true, when you think about it enough. ''Light was right:'' there was still one man courageous enough to stand up against Wily's oppression.
** Terrifyingly, Wily was ''also'' right: ''it means nothing time and time again.''
** The infamous 'we will be/BUILD heroes' line. Both Doctors do what they believe will make them heroic in their own eyes- but Wily is the one who takes the more personal role by becoming a hero in the public eye, while Light builds his heroes.
* Protoman claimed humanity would never be willing to stand for itself. However, the prequel album presented Joe - a human who died trying to fight against Wily. This means that Light never told Protoman anything about Joe.
** He also never told his sons about Emily, as she's never mentioned in Act I.
* Act II starts 30 years prior to the events of Act I. Assuming this means 30 years before Protoman was completed, it means that Breaking Out onward takes place 18 years after the first part of the album. This means that [[FridgeHorror the oldest that Joe could've been was 18,]] [[AdultFear or, more realistically, 16 or 17.]]
* Notwithstanding the fact that Joe was probably a little too hot-blooded for his own good, it certainly seems strange that he accidentally blows himself up. But the liner notes make the detonation source ambiguous. It's entirely possible that Wily, being the CrazyPrepared man that he is, set ''his own'' explosives on the tower years before, waiting for the day when someone would try to shut them down, so that he could set off the explosion himself to institute martial law, and also take care of a potential rebel/hero.
* The entirety of ''The Fall'' strikes with terrible FridgeHorror power: The song is uplifting and hopeful, and Joe ultimately succeeds in his mission according to the story. However the lyrics explain the truth of the matter: climb to the top of the world, and you will see that when you fall, you fall from a height no man has ever known. ''But you still fall, and you're still dead''.