The Protomen/WMG

Protoman's Face Heel Turn wasn't because of anger at being abandoned by Man.
This one's not even that wild. Protoman turned evil, not because he thought humanity was no longer worth saving, but because his programming gave him no choice.

A line early on in Hope Rides Alone describes him as " A perfect man, an unbeatable machine, hell-bent on destroying every evil standing between Man and freedom." When he saw at the end of that song that it was Man standing between Man and freedom, all he could do was destroy that evil by Killing 'Em All.

Alternatively, Protoman never actually turned evil, and was a Hero to the end.
After being rebuilt by Wily, Protoman re-evaluated his priorities, and drew new conclusions. Realizing that Man would never truly be free until it claimed that freedom for itself, Protoman purposely crossed the Moral Event Horizon over and over again, trying to goad Man into rising against the robots through his brutality. By the time Mega Man attacks Wily's fortress, Protoman has resorted to taunting and insulting the crowd in an attempt to make them stand for themselves; note that the only damage he causes during the final battle is to his own side. Pity his plan didn't work.

Protoman would have turned on Wily in an instant.
If one. Even *one* Human had stood up and said he would fight. It was the refusal of anyone to go up and fight beside him that caused him to defect. He does seem to practically beg the crowd to rise up. Prove him wrong. That he wasn't supposed to just be a martyr. That he was the 'hero' of man. One whom could rally them to fight for their lives. And its highly unlikely that he'd have stood there and tried to dissuade Mega Man from fighting if Wily had truly rebuilt him. Seems far more likely that he'd have just shot him and moved on. Wily certainly seems to have realized there is no longer a need for subtlety. Why have a robot running around capable of destroying a great many of his hordes of underlings? Order Proto Man to shoot him and move on. Although Wily may believe that once again, One robot won't make a difference.
 * Jossed. When someone actually does stand up for himself, Protoman just flips him off.

Protoman wouldn't have stood down just because someone from the crowd stood up
His dying words are "...A hero is just a man who knows he is free." If a member of the crowd stood up just because he told them to, on pain of death, they'd still be doing it for the wrong reasons-- because someone else told them to. The only thing he could do was either kill Mega Nan and force them to defend themselves, or be killed by Mega Man, hoping that his death inspired the people to stand up for the right reasons.

Dr. Wily is either a robot or a cyborg by the time of the Sons of Fate.
He knows he's not getting any younger. After seeing what Joe and Protoman could do, he grew paranoid, and decided to make himself live on forever through the use of robotics or cybernetics. Not only that, Turbo Lover, the guy who voices him, was seen wearing an arm cannon at one of their shows...during the Sons of Fate.
 * In an interview with the band, the interviewer asked if Wily was human. Wily's response? "Barely."

The Narrator is band member Heath Who Hath No Name.
Well, the character himself is nameless...

Protoman is trying to warn his brother in The Stand.
Do you understand now?/Do you see the truth is/They don't want to change this/They don't want a hero/They just want a martyr, a statue to raise...
 * Protoman does seem to love his brother; he meets Mega Man's eyes in the liner notes and embraces him when he dies. His angry words in The Stand, although motivated by the desire to goad humanity into attacking him, are also to warn his brother: he doesn't want Mega Man to suffer the same fate he did, being "killed" and his ideals broken.

Dr. Light told Mega Man not to fight as a test of his resolve
Proto Man defected to Dr. Wily's side when he realized that he fought alone. Dr. Light, realizing that they needed to fight regardless, told Mega Man that fighting was pointless. If Mega Man agreed, then he was like Proto Man. If Mega Man disobeyed, then Dr. Light knew that he was the hero the city needed.

Protoman never cared about the fact that men refused to stand. The only one he cared about was Dr. Light
Dr. Light didn't fight at Protoman's side. He didn't step up to aid Protoman when he was being torn apart, he stood there and watched like the rest of humanity. Protoman is using a plural, but all of his accusations against humanity apply directly to Dr. Light himself. There's also a fair amount of evidence that some random human standing up to oppose Wily wouldn't have worked, Protoman was waiting for a specific person to stand up and put their own life on the line.

The bitterness and hatred don't stem from being abandoned by people he never cared about in the first place, they come from being abandoned by his father.

Wily wasn't talking about robots...
When he said "If you replace the working parts you get a different machine; he was talking about society. The "working parts" are humans, because they do the work, so he's basically saying that a society ruled by robots is still doable. So when Light says "If you destroy the working parts what you get is a broken machine" he's saying that if humans get slaughtered then society collapses.
 * Alternatively, Wily was talking about humans because before he and Light activated their robot army, humans were the working parts, i.e. they did all the work that made society function, e.g. working in the mines like Light's father. By replacing the working parts (humans) with different parts (robots), you change the machine (society). Later, when Light talks about destroying the working parts, the working parts aren't humans; the wheels of commerce and industry are turned by robots now, so he's talking about destroying the robots in order to break Wily's control over his decadent and morally bankrupt society. This also harks back to "The Good Doctor"; Light talks about using the new robot hands to "destroy" and "rebuild". First robots were used to destroy the society in which Light grew up and rebuild it into Wily's society, then Joe and Light (humans) tried to destroy Wily's society in order to restore a more human and meaningful one.

Act 2 is a dramatization of a Tabletop RPG game.
Joe died cause he rolled a 1. Meanwhile, Dr. Wily has a bonus on his Charisma stat.
 * Emily rolled a Will save when confronting him, but failed a grapple check. Though that's not hard to do.

Joe is Light and Emily's son.
Even the math for this works out; about 18-20 years passed between Give Us the Rope and Breaking Out. Joe's about that age. It would explain the bond between him and Light...
 * Something's gonna be Jossed, because if the song "The Message from Dr. Light" by The Megas does take place in the same universe, Dr. Light never had any real children and therefore wouldn't be Joe's father.
 * Unlikely, as the Megas are clearly working with a separate universe from the Protomen.
 * In the liner notes for "Breaking Out," Joe says that his mother has only been gone for 3 years, and lived in a house. At that time Emily had been dead for "a generation," and she had lived in an apartment.
 * Just because Joe grew up knowing that woman as his mother doesn't mean she's necessarily his biological parent. Emily could have died when he was a baby, and with her gone and his father in exile, Joe would have to be raised by somebody else, namely the people mentioned in the liner notes.

Joe was drunk the whole time
At the very least, long enough that it was too late for him to back out. Consider this-- When Joe's introduced, we find him in a bar, boldly proclaiming "I'm breaking out of here tonight!" He stumbles out, hops on his motorcycle and swerves through the streets, eventually getting into a knife fight with the Sniper Robot. After Dr. Light finishes it off, they start chatting about how someone should do something about Wily, Joe's still got enough liquid courage in him to think he can. The two have a few drinks at Light's while plotting to "Light Up The Night" and Joe, with his pack of explosives, rides drunkenly through the streets and up the stairs of the broadcast tower, fumbles the detonator when removing it from the bag, and accidentally activates it, prematurely setting off the bombs.
 * It would explain "... this burning like my veins are filled/with nothing but gasoline.", it's alcohol!

Joe killed himself
Dr. Light says it best in Here Comes The Arm- "I think somehow, Joe knew it. Paid the price he thought he had to pay...". Joe either knew the plan would fail or thought that should it fail, he'd be killed by the robots. Deciding that it was Better to Die Than Be Killed, he detonated the bomb while he was still on the roof.

Joe is Wily and Emily's son.
For irony's sake. Also, consider this. "Wily: Don't turn your back on me! Joe: Don't turn your back on the City..."


 * Then again, why would Wily name his sniper robots "Joe" to spite Dr. Light if it was his own son?
 * Who says he knew that particular Joe was his? Even if Wily knew that Emily's child was son and not Light's, it's unlikely that Wily would have kept track of him after her death. It'd be nicely ironic for Wily to do the math later and realize that the son he had forgotten about was the only human willing to take a stand.
 * Because the green Cyber Cyclops is not called Sniper Joe. It is only ever refered to as the Sniper Robot. When Joe disguises himself as one to get close to the tower, then he becomes Sniper Joe.
 * Actually, according to the liner notes, he started calling the Sniper robots "Joe" after the incident as a way to get at Light.

Joe is Protoman.
To understand this, one must know that the games' Sniper Joe enemy was based on the original prototype, AKA, Protoman himself, thus making Protoman the original Sniper Joe.

Joe rebels because he has fallen in love with the city and doesn't want to see its people suffer Wily's silent oppression any longer. The motorcycle he uses to leave the city belonged to Dr. Light, his metaphoric father. The reason he wasn't able to match up to "Light's Monster" was because Wily had upgraded and modified the Sniper Joe's designs as the years went by. Light said that he built it metaphorically because he still felt the guilt of not stopping Wily before everything started. It is also noticeably suspicious that Light would not only trust Joe so quickly, but be willing to let Joe risk his life so readily and can be explained by Light recognizing Joe as Protoman and realizing that Protoman's presence and use of his metaphoric father's motorcycle meant that Protoman had betrayed Wily to free the people of the city he came to love.

"Hope Rides Alone" is a propaganda retelling of Joe's mission to destroy Wily's control tower by a human resistance written in-universe after the events of Act I.
 * At the very least, Protoman's helmet is Joe's repainted. It was bestowed upon Protoman as a tribute to joe's sacrifice and a symbol of his courage.

Joe is the Green Biker Dude from Mega Man X 2
. Green biker's helmet, dies by explosion...

Light and Joe's plan wasn't the only one happening that night.
Joe inspired the girl in the bar to go out and try to change things too.

From "Breaking Out" to "Light Up The Night", there's a female background singer, echoing a few of the lines from each song- If put together, they almost sound like they could chronicle a plan being executed or a resistance being formed.

In "Breaking Out," they're first phrased as questions while he's talking to her - "Something's gotta change?", "Something's wrong here?", then as statements as he leaves "Don't turn your back on the City!" and after he's left-"...nothing but the static. If you can hear me- Don't turn your back on the City!"

In "Keep Quiet", she sings the ominous chorus- "This City, she's been dead for years now... So death is not something that scares me... There's worse things than death here. Keep quiet."

In "Light Up The Night", the actual plan is made and attempted- "At the heart of the City. The man in the tower controls it all. It's like they gathered up the City and now... It's gone to hell and we wonder how." "Now the wheels are spinning out of control... if we destroy the working parts... a beacon of light from a burning screen." "Light up the night!" "There is a fire that will burn through the streets of this city, and we will stand in the light, we will stand in the light!"
 * Well, the liner notes just say 'Human Choir', and for Light up the Night we can assume it's Emily; note she only comes in when Light is singing.

Joe suffers from a terrible case of Acne.
It would explain why he's always wearing a helmet. There's a reason why his song's called "Breaking Out", you know.

Joe is just hiding.
Cause he's too awesome to die.

Alternatively, Joe's body was taken in by Wily.
Cause he was that awesome.

Wily wasn't interested in Emily herself, he saw her as disruptive influence.
Before Emily, there were just Light and Wily. Wily, sly as he is, probably had the trusting Light wrapped around his little finger. Then the strong-willed and more down-to-earth Emily came along and called his BS, subsequently making Light suspicious of Wily as well. So Wily decided she had to go... and then things got a little out of hand.

Wily has two personalities, evil and good, that he rapidly shifts between.
Listen to "The Good Doctor" again. Notice how, half the time, Albert is trying to keep Thomas from performing an act that would cause massive upheaval in society, and the other half he wants to control it. Nite that, he seems to change between the two very rapidly, as he changes his mind between the lines "Men would cower at the sight" and "Man was not built for such a height!", and again before "We will build heroes!" He also seems to regret what he is doing in "The Hounds," (If there ever was a time/If there ever was a chance/to undo these things I've done/ and wash the bloodstains from my hands") but then dips into megalomania again ("If you think that you can run/If you think that you can stand/ you forgot who turned this city on/YOU FORGOT WHO PLUGGED THIS CITY IN!!").

The girl in the bar was working for Wily.
She finds people expressing negative opinions of the City and sends the Sniper to eliminate them.

It's going to get better.
For all the deconstruction and doom and gloom, the later series had humanity stand alongside the heroes. They might not have been as effective as the heroes, but they were not sitting on their asses (especially Ciel), and by ZX they were an active part in the fighting.
 * Calling it now, Act III involves Mega Man's adventures outside the city causing a change of heart that makes him decide he shouldn't turn his back on the city just yet.
 * The resistance confronts Dr. Light and asks him to make them capable of holding their own. Seeing humans (albeit modified) willing to take the fight to Wily rekindles Mega Man's spirit, but Wily has built his own super robots in the mean time (read: the Robot Masters). However, Mega Man fights them nonetheless and though many (if not all) of the warrior humans die in their struggle, knowing that they would at least take a stand allows him to push through and defeat Wily and his Robot Masters.

Act III will be a pre-prequel.
It will describe Light's childhood, and the prophecy that he would restore balance to the city. It will emulate the music of the late 30's and 40's.
 * Jossed; it takes place after Act I.

The girl Joe kissed in the bar will return in Act III.
And it will be revealed her name is Roll.
 * Considering she'd be at least fifty by the time of Act I, I'm not so sure.
 * Thirties, at least; Breaking Out is 18 or so years after Give us the Rope and it took 12 years to build Protoman. So there'd be 12 years at least.
 * Jossed; Roll is the third creation of Dr. Light. It's doubtful the Protomen would completely ignore that detail.
 * However, Roll still might be introduced in some other way...

Act III will end with Wily still in control.
He won the first two times...

In Act III humanity would find redemption
As Protoman wished in Act I, the surviving humans of the massacre will tell the story to their children and they will grow inspired by it, forming a resistance. This may cause Mega Man to have a change of heart about humanity, and together they will be able to defeat Wily.

In Act III we will discover that the true hero was always Dr. Light
As he is the only human who still remembers how it was before Wily was in power, and the only one beside Joe who is willing to do something about it.

Act III will involve Rush.
Remember the end of Due Vendetta: "Sniper Joe! Rush Jet! Doctor Light! MEGAMAAAAAN!"

Protoman will return as Zero in Act III.
Wily rebuilds him again, but this time he abandons everyone's goals. There are no (H)eros' left in man, and such.
 * Jossed; The Protomen have stated they will not go into the X series; band member Commander has expressed outright dislike for it. So no Zero.

Protoman will return as Bass in Act III.
Except, Protoman has been wiped and has been reprogrammed into Bass, with a Black and Purple paint job to boot. Protoman wasn't destroyed, just killed, or as much as an android could be killed. For all we know, all he may have needed was a new power source and some new parts.
 * {Probably} jossed, as the Protomen have declared "Bass is stupid" at least once in an interview. Still, Proto being him would work better than a new character, so...

Protoman will return Act III but without his heart.
Dr. Wily will take his body and reprogram it, to have no personality/soul/heart. Prompting Mega Man to return from self-imposed exile not to save humanity, but to finish Wily once and for all.

Act III will end with the death of Dr. Light.
This is actually an opposed to Dr. Wily will win. Dr. Light will complete his mission in life, but won't live to see the after effects.

Its gonna get real bad, real fast.
Humanity is only incited to even call for Mega Man's help when it is facing wholesale slaughter at the hands of Wily at the end of Act I. Mega Man will realize this and see that humanity has not and will not change, it is as selfish as ever in his eyes. Also, Panther has mentioned that he doesn't envision the story ending well for humanity.

Dr. Wily will kidknap Kalinka Cossack and focre her father to help him improve his robots.
Both Acts I & II take a piece of what little story Mega Man has and runs with it. We already have "Mega Man had an older brother who was thought to be dead but is actually working for Doctor Wily" and "Doctor Wily used to be friends with Doctor Light, but betrayed him," so we are left with a few options. "Wily escapes from prison again" can't work since he is still in power. "Wily pretends to reform" wouldn't either (again, he is still in power, plus he has long since crossed the Moral Event Horizon). So the plots of 1, 2, 3, & 7 are all out. So is 6, since he doesn't need to trick people to take their robots. So we are left with 5 ("Protoman attacks again"), part of 8 (Duo and the Dark energy), and 4. As Protoman is dead, 5 probably won't happen, and there are no fantastic elements in the story aside from the robots, so 8 isn't likely either. In 4, Doctor Wily kidnaps Kalinka and forces her father to work for him. This is very much in character for Protoman!Wily. He may even rise up and help Mega Man beat Wily, serving as a man on the inside.

Act III's heroes will be the Protomen themselves.
Detailing how they united against Wily (with Mega as their leader.) and came back to our time to warn us about the events of Act I and Act II.

Act III will involve the manga canon's Heel Face Turn of the original Robot Masters
Capped off with one hell of an Ironic Echo on Light's part as he reveals to Mega Man his 'Brothers in Arms'

"If you replace the working parts, you get a different machine."

The Yellow Devil is going to be in Act III
The Sniper was already a major villain in Act II, and the Devil Series are really the only other notable Mega Man enemy who isn't Wily or a Robot Master.

Thee will be a resistance movement calling themselves The Protomen.
In honor of the fallen hero. It will also serve as a nice Title Drop.

Everything is leading up to a final confrontation between Wily and Light.
From the start, everything has been pointing to man needing to stand for itself, something stated outright by Protoman in Act I. The only thing any of the known robots have done is cause a problem. First was the one Wily and Light build together, which Wily later used to kill Emily. This paved the way for his takeover of the city. Second was the building of Protoman, and Protoman's attempt to save mankind from Wily's rule. Wily simply used this as an opportunity to get a new secret enforcer. Finally, there's Mega Man. If he hadn't left the relative safety of the apartment to try and avenge Protoman, he never would have damned the people of the city to wholesale slaughter by Wily and his robots. So, Light will, eventually, gain the resolve to take on Wily himself. It will be the only way to defeat his old friend once and for all.

The Protomen are from the future and led by Mega Man X in disguise. They sing about the future to keep us from making the same mistakes in our timeline.
The opening to Hope Rides Alone is sung from the perspective of a third party who does not speak on any other track on the album. This is X himself, telling us of humanity's fall in his own past.

In past interviews, The Protomen have admitted to being from the future, but have mysteriously changed their story after the tragic losses of their original drummer (Demon Barber) and their base of operations (The Thundercon).

The band's secrecy does not help matters. No one truly knows how the band originated, and posts made on their message boards are often edited to cover up anything from a leaked mp3 to calling the wrong movie "cheesy". Even messages posted by the band members themselves aren't safe from these mysterious edits. For instance, on one occasion Demon Barber returned from the grave to reveal a secret to the board, but his post was soon replaced by the undead chanting of "brains". Soon after, it was announced that his permanent replacement goes by the name "The Reanimator".

It should also be noted that Demon Barber was never seen without a large "X" painted across his face.

K.I.L.R.O.Y. is Joe.
He survived the fall from the tower, face badly burnt and scarred in the explosion. Faking his death, he went into hiding, using a robot mask to conceal his features. (Plus avoid any spy drones.) Eventually, he met the rest of the band, and filled 'em in on Act II.

Dr. Wily is already dead.
Dr. Wily is either already dead or will die of natural causes before any solid form of resistance from man can finally rise against him. The people were kept in line by fear of the machines alone, and the machines were just following their programming from before Wily died. In other words, they were free of him without ever knowing it.
 * Jossed; in some of the Protomen's live shows, Wily personally orders his robots to slay the crowd after Mega Man kills Proto Man in "The Sons of Fate."
 * True... but this is really only how it is presented by the Protomen. They are not the characters themselves, they are merely troubadours bringing us the tale. Perhaps they do not know any better than we do.

The Megas' song "The Message From Dr. Light" takes place in both that and this universe.
It takes place either just before or during Hope Rides Alone or just after Unrest In The House Of Light, depending on which robotic son he was talking about.
 * In the narration written in the album insert, it says that Light only realized after Proto Man was already dead that he thought of him as a son. Until that point he'd seen Protoman as nothing but a weapon. That's the main idea of Funeral for a Son. So it couldn't be Proto Man, he would have to be talking about Mega Man for this to work.

The song Beard's Going Nowhere is written by Dr. Light.
It was written during a period between his exile of the City and saving Joe. Dr. Light has gone somewhat insane after losing both Emily and the destruction of man, so to cope he creates fantasies within his head. Details are as follows: Alternatively, Light is singing to Emily before Act II. It comes off like a rather drunken love song. "Beard's Going Nowhere: We can get out of this town before we both get too old. The State Vs Thomas Light: Will our souls remember where we said we'd meet on the way out of this town?"
 * The fact that 'the City' wants him to shave is his own antagonizing of Wily, and belief that he is turning the city into a Facist state, rather than apathetic and fearful of the Robots.
 * He tricked himself into believing that Emily didn't die, and the fantasy is that they are leaving. The rambling at the end is either something 'romantic' that he is saying to her, or he has gone off the deep end.
 * When he says that "I'll finally be a man" he means that he will stop Wily from enslaving the City, and "man" up to the problem that he ignored.

Beard's Going Nowhere is the Alternate Universe Happy Ending.
Where Light and Emily left the ruined City and escaped into the fields...

Beard's Going Nowhere is a prequel.
It mentions Emily, so it has to happen before "The Father Of Death." There are also references to the fact that The City has the same worker's rights as the beginnig of the Industrial Revolution, yet is in a future advanced enough for robots, and you can imagine that it was a Crapsack World before Wily got his hands on it. Now it's as bad as it was before, plus Orwellian surveilance.