Dr. Weil from Mega Man Zero has the dubious honor of being the biggest Complete Monster in the entire 'series. Not even Wily, Sigma, or even Regal (a fellow Complete Monster himself) can match him in sheer malevolence, insanity, and depravity.
Here's the lowdown in case you have to ask why he's here instead of any of those three. First, between the Maverick Wars and the Arcadia Wars, there was an incident known as the Elf Wars, triggered by Dr. Weil corrupting the Mother Elf - a sentient superprogram made to eradicate Wily's Maverick/Zero Virus - and making her into the Dark Elf and using her, along with smaller copies known as Baby Elves and a reprogrammed Zero's body, now christened Omega, to elevate him to a position of absolute power in a campaign of mass terror. Why? Because he thinks that humans are superior than Reploids (and, according to his claim, he's grown tired with all of the Maverick Wars). And that's after the real solution of peace had been found and successfully used - the Mother Elf itself.
By the time the Elf Wars ended, 60% of all humans and 90% of all Reploids alive before the war were wiped out, the Dark Elf had been entombed with either a massive cipher device or X's body, and Weil was given an undying mechanical body before being jettisoned off into space so he could watch the world prosper without him. This is just the beginning and take note that HE STARTED EVERYTHING.
One hundred years later, he drops down with Omega back online and has managed to construct a replica of X - unlike the Continuity Snarl of the first game, this one is clearly a copy - and wormed his way into supreme power that way, going so far as to have the Four Guardians dismissed. Then, he drops a high-yield bomb in a human settlement with Omega, Crea, and Prea on board, just to get his hands on the Dark Elf again! When Zero comes along to disable Copy X, he kills himself in a One-Winged Angel attempt, thus putting Weil at the top of the food chain as he planned all along. The Resistance later avoids a mass brainwashing attempt by Weil using the Dark Elf's power, though at X's ultimate expense, long enough for Zero to shut down Omega and purify the Dark Elf completely.
Even with Omega dead, Weil still rules Neo Arcadia, and his iron- and spike-fisted rule is so brutal that humans are risking going into the wastes of the outside world just to get away from him. Why does he do that? He thinks both humans and Reploids must pay for the crimes they committed against him, even if it's blatantly obvious that he is the one at fault! A caravan of such refugees, led by Neige, finds Area Zero - the site of the Eurasia colony crash - and begins setting that up as their "home away from home", only for Weil to send troops along to start to interfere with the region's recovery as a diversion while he gets Ragnarok up and running. When Craft heel-faces, blows up Neo Arcadia, and then wrecks Ragnarok's cannon controls, Weil tries to drop it on Area Zero as a last resort to kill the whole region, if not the whole planet. Zero manages to stop this completely, though, unlike in the X series, this really was his last hurrah.
Though this last entry may go into Wild Mass Guessing territory, it is backed by some rather disturbing evidence. By the actions of all Maverick parties after the end of the Arcadia Wars, there is a very strong possibility that the real Big Bad isn't Serpent, Master Albert, or even Master Thomas, but Dr. Weil himself, still alive inside Biometal Model W. Akin to the Jenova Reunion, Albert's plot to become the ultimate Mega Man involved gathering all the pieces of Model W to construct a new weapon with which to cleanse the world as its new god. It is likely he lost his soul to Model W during his initial research in the same way Serpent lost his due to his own use of it. Indeed, the plots of Serpent and Albert in the ZX games, as well as Thomas' coming plot, all parallel Weil's in some fashion.
At the end of the day though...it comes down to this; although he ultimately failed and they won...Weil killed both X and Zero in a way. And he did all that because he thinks if anyone doesn't follow him, they deserve to die. Compare with Wily, who just wants to Take Over the World and stops there (Weil takes over the world...and make the people suffer even more!), Sigma who actually started out as a clean-cut, respected Hero, but fell victim to The Corruption, but still at first tried to do everything for the Reploid's welfare (Weil exhibits a very severe case of It's All About Me and cares NOTHING about humans and Reploids all the same). If that's not a reason by itself for a character to be a complete monster, I don't know what is.
Keep in mind that Weil existed for only two games, although you can make it four if you count the ZX series, and the rest of his atrocities are only revealed All There in the Manual. And yet, it's through those two games that he quickly gets through to the top of the Sorting Algorithm of Evil, beating Wily and Sigma so easily, all because his acts during the games are horrific enough; mere mention of All There in the Manual takes his monstrosity to the extremes. His actions and war were SO horrific that Neo Arcadia actually hid that part of history, going so far as to flood libraries and declaring anyone who found out a maverick, just so nobody could repeat "Weil's Sin". There's also the little fact that Capcom tried to humanize Wily and Sigma by uncancelling and (although scrapped) retooling their respective series to directly contrast Weil. That means the developers recognized (in other words, they knew) Weil is the most evil villain in the entire series. Sorting Algorithm of Evil, indeed.
Although the Rockman Zero manga was intended to be more jovial compared to the actual Zero games, Dr. Weil's characterization in that manga is just as monsterous. Like in Mega Man Zero 3, he was searching for the Dark Elf. At one point, he also emerges from underneath Lito's house to fight Zero, nearly killing Lito, and thus getting Zero extremely angered. He ultimately gets his Karmic Death when Zero smashes his chemical container, which was supposed to keep Weil alive.
It speaks volumes when his dragon (Omega), who has a MONUMENTAL (and by monumnetal, we mean most of humanity) body count worth of people who he has personally killed, isn't considered a Complete Monster. Then again, his crimes simply amount to being a mechanical Khorne Berserkeron 'roids. As a matter of fact, the fandom loves Omega in a form of heel hate. Contrast with Weil, who the fans simply hate with the burning passion of a thousand suns.
Weil is even acknowledged as one in-universe: Basically, after Zero stops Pegasolta Eclair's attempts at dumping acid rain on Area Zero, Ciel remarks that she couldn't believe that Weil was even human to begin with.
Gemini, from the first game, kills one of his allies for no reason when he could've easily helped her and defeated Mega Man. He also manipulates a boy with multiple personality disorder into helping him to blow up the entire planet and is revealed as the one who manipulated King Cepheus into destroying the AM Planet. In the anime, he brutally murders the FMians, who had been made rather sympathetic and likeable during the season, for energy (the worst being when he killed Wolf while he was watching a girl he had befriended) to power Andromeda, then his other half when he failed to kill Cancer.
On the anime bit, keep in mind that it's not just Gemini who's the complete monster. That part about him killing his other half? The half who does the killing is the human half of Gemini: Tsukasa, who was left to die in the blaze of a car accident. In the games, Tsukasa has an Ax Crazy split personality named Hikaru; in the anime, Hikaru doesn't exist and it's all Tsukasa. What makes it worse is that, in the rushed Finale, Tsukasa simply gets his mind wiped and stripped of his powers.
Joker, from the third game, coldheartedly kills Luna, laughs about it, and calls her "a stain upon the Earth" for being without powers. Even his allies are shocked. He also tries to make Ace go Crush Kill Destroy later on.
King is even worse. First of all, he's Joker's operator, so all of Joker's actions can ultimately be traced back to King. Second of all, he is willing to use and manipulate anyone for his own good. In addition to forcing his own Wizard to self-destruct to defeat his enemies, he adopted orphans and forced them to undertake suicidal missions in order to further his own plans. In fact, it is said that Jack and Tia were the only orphans to survive these missions. He then proceeded to take control of Meteor G so he could take over the world by force, raining down deadly Noise upon those who would not subjugate themselves to him. However, after being betrayedbyhis subordinates, King is supposedly destroyed, but actually becomes an Energy Being and decides to wipe out the world using Meteor G because he figures that if he can't rule the world, he will destroy it. Actually fighting him head on is quite satisfying to say the least (every other main villain thus far in both the Battle Network and Star Force series has been The Unfought).
Plant Man, from the third game, who caused all kinds of mayhem in one of Electopia's main hospitals and was directly responsible for almost causing the death of an innocent child whom series protagonists Lan and Mega Man had befriended earlier. His callous disregard of human life is just as infuriating as the fact that he's trying to manipulate his operator, Well-Intentioned Extremist Anetta, into becoming just as cruel as he is.
Dr. Regal debuts in the fourth game as a Card-Carrying Villain with a somewhat nonsensical Xanatos Roulette...but it's in the fifth game that the true depths of his evils are revealed. His organization, Nebula, is devoted to converting the world to evil, causing wars, mayhem, and whatnot just to demonstrate his viewpoint - that Humans Are Bastards and, in fact, they should strive to be as cruel and horrible as possible. He also subjects Lan's father to an horrifying Cold-Blooded Torture and gleefully turns innocent NetNavis into servants of evil, slowly corrupting the whole Net. To be fair, the fifth game ends with Regal pulling an Heel Face Turn and becoming a model citizen, which would theoretically take him out of Complete Monster territory...but when you consider that said redemption only happened because he was subject to Laser-Guided Amnesia...yeah.
Want to know the reason for his Laser-Guided Amnesia? It's because Lord Wily, his father, disapproved of Regal's actions and took them away as punishment. Yes, that's right. Even Lord Wily, a person notorious for running a cyberterrorist organization as revenge on a scientific rival and nearly destroying the world as a result of using a prototypecomputer program to the Internet, disapproved of Dr. Regal's actions and made sure he paid for it dearly. If even someone like him disapproved of his actions, Regal sat quite nicely in that trope. *
But as mentioned above, he still couldn't beat Weil in terms of depravity.
It is difficult to be both a Knight Templarand a Complete Monster, but anime-only character Slur, The Dragon to Big Bad Duo, delivers. Apart from being an absolutely broken Villain Sue, Slur is also fanatically devoted to exterminating all evil from the universe...where by "evil", she means everyone who doesn't agree with her master's extremely draconian concept of morality. In other words, Slur wants to kill all humans just because she doesn't like us. And unlike Duo, Slur has no sense of fair play - she deliberately "sabotages" the Humanity on Trial plot of Stream by giving Asteroid Navis to evil people, so that Duo will be convinced that Earth doesn't deserve to live. Vicious, sadistic, and with no redeeming qualities at all, Slur might very well be the vilest Battle Network villainess ever.
Which makes it VERY satisfying when Bass impales and kills her with his bare arm towards the end of the season. Sure, Bass was just serving his own ends, as usual at the time, but you will nonetheless still cackle with glee at her expression during her horrible, well-deserved death.
And yet, in spite of probably being closest on the pedestal of evil to Weil, she STILL doesn't hold a candle to him in evilness.
The Mega Man cartoon had Dr. Wily himself, having attempted to send the moon out of its orbit to kill off most of humanity, forcing the survivors (if there were any) to consider him king, so he could prove he was better than Dr. Light. This alone doesn't qualify him; he's also tried to use earthquakes to destroy cities, threatening to destroy them if they don't obey, and he's tortured Mega Man mentally twice in the show, first by making him wonder if he's just a mistake created by Dr. Light, the second time making Proto Man be a Heel Face Mole. Even Proto Man considered this act wrong during the plan. And he ordered Proto to kill Mega Man after this.
