Complete Monster/Shin Megami Tensei

The Shin Megami Tensei Series has been around for a long time, so it's no surprise that among its Loads and Loads of Characters, we find some completely monstrous villains.

Main Series

 * YHWH himself is depicted in this light. He nukes Japan in a bid to get all of humanity praying and worshipping Him in mindless obedience. Doesn't work. So instead, he floods the entire planet. How bad he gets? In Shin Megami Tensei II, everybody wants him dead. Everybody. Even the angels.
 * In Shin Megami Tensei II the twisted versions of Archangels Michael, Uriel and Raphael are overlords of the theocratic dictatorship that has overthrown Tokyo After the End. Dividing the city into five districts, their Propaganda Machine claims they did so in accordance to the division of labor, but it is clear they favor the wealthy Central District and feel free to neglect, abuse, and slaughter outright the residents of the other four. When signs of rebellion appear in the Valhalla district, they order the Demon Lord Abaddon to devour it whole, promising to restore his angelic status if he did so; when he is finished, they cast him back into the demon world. The entirety of the Arcadia district has been lobotomized and plugged into Lotus Eater Machines, causing them to believe they live in an idyllic paradise while their physical bodies waste away; Aleph is subsequently informed the the Archangels intended to do the same to the entire planet. The workers of the Factory District have been brainwashed into slavery by the song of a Siren, who is routinely tortured by the Archangels' henchmen to keep her singing. Finally, they attempt to get Aleph and his comrade Zayin to surrender to them by holding the entire Holytown district hostage, threatening to cut off their air supply and slowly suffocate them to death.
 * Mr. Tayama from Shin Megami Tensei IV began as a small-time Yakuza leader in Tokyo, but in the power vacuum following an apocalyptic war he seized control of the city via commandeering the Yamato Perpetual Reactor, Tokyo's main source of power. He thus established himself as the unquestioned leader of the city. While Tayama protects the citizens from the hordes of demons ravaging the city, he does so mainly for the sense of power it gives him; anyone who questions his rule is killed or worse. Tayama invented a Fantastic Drug called Red Pills, that can be used to pacify demons, but unknown to the people of Tokyo, the drug is made from human brains extracted from innocent people his cartel the Ashura-kai] periodically kidnap and raise in a "human farm" until they die. Tayama is also breeding child slaves for this purpose. Though Tayama claims this is for the benefit of the greater population, he has also hypocritically cornered the market on smartphones, through which demons can also be tamed without causing harm to either them or humans, even demolishing an entire neighborhood to maintain his monopoly.

Strange Journey

 * The greedy Captain Jack from Shin Megami Tensei Strange Journey proves that even in the demon world, sometimes the worst monster is humanity. A Mercenary loyal to nothing but his own pocketbook (in his mind, it's the only thing with any permanence in the world), Jack is hired by an unnamed client corporation to pillage the demon world of its natural resources, a job he takes a twisted pride in. Though initially appearing as an uneasy ally to the protagonists, it is eventually revealed that he plans to manufacture a demon army for his client and himself, regularly performing painful amputations on any demon unfortunate enough to fall into his clutches and fusing them together into unstable forms that leave them in constant pain. Jack's worst action, however, is fusing the protagonist's ally Jimenez - a human - with his Morality Pet Bugaboo, resulting in an extremely violent Half-Human Hybrid who causes many more horrible things to happen later on in the game. When finally confronted by the protagonist and Jimenez, Jack's only action is to scold them for costing him valuable men and equipment before engaging them in a final battle.
 * Mitra is An Evilutionary Biologist trying to find a way to induce the perfect insanity in humans. He succeeds. Through repeated testing.

Devil Survivor

 * Jezebel in Devil Survivor. In life she was a wicked, manipulative woman who used her position and power to convince her people to worship the evil Phoenician god Baal, as well as having an innocent man murdered so her husband could steal his property. Now she's been reborn as a demonic minion of Belberith and gradually corrupts Amane.
 * Amane's father Kuzuryu might count too. He begins a huge cult, allows Jezebel to possess his daughter and creates the bloody mess that is the Yamanote Lockdown to summon Belberith.

Digital Devil Saga

 * Serph Sheffield is a Manipulative Bastard who manipulates everyone and anything around him, including convincing an innocent girl called Sera he honestly cares about her, all in his quest to reach the power of God) He uses Sera's growing love for him to push her Psychic Powers into further maturation, only to express disgust at Seras creation of a virtual paradise consisting of AIs she uses to escape the pain of his experiments. When Colonel Beck proposed to change Seras paradise into a training simulation for creating stronger AIs, Serph overrides Heat O'Brien's warning against destroying Seras mental condition and tells Beck to proceed. After a desperate Heat pulls a gun and demands the project to stop, Serph tells Heat that a human's mind is no different than a machine, and that his subjects, including Sera, were expendable and could be replaced, before manipulating Argilla into killing Heat. After being turned into a demon by a heartbroken Sera, sending a massive data surge into the now black Sun, Serph goes on a killing spree starting with Beck and Argilla before being killed offscreen. Refusing to accept that he is dead, he re-appears at the EGG facility as Solar Data and tries to kill the AI Serph and Heat while proclaiming to have the power of God. A cruel and manipulative young man, his actions are largely responsible for the disasters plaguing the series.

Persona series

 * Persona 3:, the heroes, as a seemingly kind, bumbling Pungeon Master. However, as the game approached the end, his true colors start to show. He is revealed to have partaken in Koutetsu Kirijo's experiment to revive Nyx, which caused an explosion that killed hundreds, including TheProtagonist's parents and Yukari's father. This brought about the Dark Hour, which killed even more. He performed unethical experiments on children to produce artificial Personas, including the members of Strega.
 * Persona 4: Arena Ultimax reveals that he even used Sho, his adopted son, for the experiment. When Sho's Split Personality, Minazuki, tried to kill Ikutsuki in self-defense, he put him in a coma and only bothered putting him on life support so that he might be of use to him again. When the events of Persona 3 begin, he manipulates the S.E.E.S. into killing the Twelve Shadows under the belief that it would extinguish the Dark Hour. However, in actuality, killing the Shadows was what he needed to revive Nyx. Nyx, being the Death Arcana, would wipe out humanity. When he was found out, he reprograms Aigis into helping him capture the S.E.E.S., which consist of teenagers and a ten-year-old boy. When Mitsuru's father tries to stop him, he shoots him dead before preparing to do the same to the S.E.E.S., and would have succeeded if Koromaru didn't stop him. A sociopath who would wipe out all life on Earth just to appease a God that is Made of Evil, Ikutsuki stands as one of the most vile human beings in the franchise.
 * from Persona 4 is revealed to be one of these, enacting the murders just for the fun of it. Of course, there are some hints of Magnificent Bastard hidden under there, according to some of the fanbase.
 * The first murder was a complete accident. He was trying to rape the victim. The second murder was for the fun of it, as well as convincing to do the rest of the kidnappings.
 * Persona 5: While Yaldabaoth set the plot in motion, this duo proves that Humans Are the Real Monsters.
 * Coach Suguru Kamoshida, representing Lust, is a former Olympian turned head PE teacher at Shujin High in Tokyo, and secretly a dangerous sexual predator. Protected by the school administration due to his past fame, Kamoshida sees Shujin as his own absolute fiefdom, and gets his jollies extorting sexual favors from the girls he teaches, often forcing one of his male students, Yuuki Mishima, to procure them for him. His male students fare little better, as when they do poorly in his classes he calls them to his office for "private tutoring sessions" that are really just excuses to beat the tar out of them; as a result both boys and girls live in terror of him. Kamoshida also indulges in pettier Jerkassery such as provoking the star of the track team into punching him as an excuse to get the team shut down, and leaking the Protagonist's criminal record to the entire school. When his "favorite" victim, Ann Takamaki, refuses to sleep with him, Kamoshida crosses the Moral Event Horizon and rapes her best friend as revenge; the girl in question feels so humiliated she attempts suicide. When confronted by the Protagonist, Kamoshida freely admits his crimes, but confident the system will protect him, types up a false assault report to have him expelled. Even after the Phantom Thieves steal his heart, he states his intention to commit suicide himself to escape justice, only submitting to arrest after a "The Reason You Suck" Speech from Ann.
 * Masayoshi Shido, a charismatic member of the Diet and representing pride, is in fact the head of The Conspiracy profiting off the other villains. Having illegitimately fathered Goro Akechi, Shido is approached by an empowered Akechi offering his services as an assassin. Having been involved in the research of Wakaba Isshiki, who found out about the Metaverse, Shido has Goro kill her so he can steal her research. Shido has a will forged blaming Wakaba's daughter Futaba for her "suicide", sending Futaba into a depression. Later, Shido sexually assaults a woman before the Protagonist intervenes, which prompts Shido to ruin the Protagonist's life in response, later remarking that he's crushed so many people he doesn't remember someone that insignificant. Shido and Goro go on to manipulate the people's faith in the government and the Phantom Thieves, with support for the government decreasing and the Thieves increasing. Once the Thieves steal the heart of Kunikazu Okumura, a patron of Shido's, Goro, under Shido's orders, kills his Shadow, ultimately killing Okumura on live television and pinning the blame on the Thieves, while Shido and Goro— outspoken critics of the Thieves— rise in popularity. Shido and Goro then hatch a plan to kill the Thieves by Goro acting as a Mole, which the Thieves see through and foil. At this time, Shido's other confidant, the SIU Director, is killed by the duo. After Goro loses to the Thieves, Samael— Shido's Shadow— reveals that Shido sees Goro as expendable. When the Thieves confront Samael, he mocks the weakness of his followers and reveals that Shido was going to kill Goro anyway despite suspecting that Goro was his son. Shido's final action before his forced reformation is to destroy his own Palace after Samael's defeat in a final attempt to take the Thieves down with him.