Pokémon Super Mystery Dungeon started out as a Slice of Life-adventure story but then came the second half in which right after the heroes found the petrified Latios and Latias, Entei shows up and threatens to kill the protagonists on the spot. While he isn't strictly villainous, any scene that centers on Entei means a flip of the off switch on the franchise's lighthearted nature and presents a clear sense of danger. Later on, Nuzleaf and Yveltal pick the torch from Entei by turning almost everyone in the world into stone.
The Ultra Beasts also spark a darker tone once they appear, with much being made of their destructive power, violent tendency and threat to both humans and Pokémon. Their postgame storyline is among the darkest plots in the series, with the implication that the International Police are using the player (who's no more than eleven) as human bait, as well as Looker telling them that if they can't catch the Ultra Beasts, they must be destroyed (not that the player is even given the option to destroy them). Even within this storyline, there's a Knight in the form of UB-05: Glutton, a.k.a. Guzzlord. It's revealed that ten years prior, a Faller used as bait was "done in" by it as a result of Looker taking pity on it. Rarely if ever has a Pokémon outright killing a human been mentioned before.
Cyrus from Pokémon Diamond and Pearl had a plot much larger in scope and a larger dark presence on the plot than the prior villains, heralding the Cerebus Syndrome that started in that game. Ever since, main villains have matched, if not exceeded, his dark presence.
Spookys Jumpscare Mansion starts off as a lighthearted parody of the horror genres overuse of Jumpscares. Then Specimen 2 shows up, and all the subsequent Specimens after show the player how how horror is actually'' supposed to be scary.
Memoria Freese: Things were already serious in the Date A Live crossover campaign Ais Catastrophe before the false Kaguya Yamai appeared after she turned Ais into an Inverse Spirit but it was only later revealed that she was behind everything that happened so far. Not only does she beat out Kurumi as the most "evil" Spirit, the humor level drops at the very moment she reveals herself. From there on, the story is dark and horrifying with psychological torment and creepy scenarios. And by a far extension, she's also one of the most vile foes Bell and Shido faced, making her name in both worlds of Date A Live and Danmachi.
The Legend of Zelda: Majora's Mask has its titular villain, a creepy and mysterious power that has an evil plan to literally destroy the whole world. Every character that interacts with Majora ends up worse off, from being transformed into a Deku Scrub, to having an entire geographic area frozen. Majora's motivations are never explored beyond an unstoppable drive towards chaos and destruction, with the central conflict of the game focusing on the impending apocalypse from the moon crashing into earth in three days. Whereas most other games in the series had their own dark villain in Ganon/Ganondorf, Majora's Mask goes an extra step by forgoing the quest for power or status that the Ganon sought and instead having Majora just want to destroy everything for no apparent reason.
The second game's Overlord Zenon is all about deconstructing the "achieved greatness through killing entire worlds to level up" archetype of demon overlords. The first time the latter is introduced, she casually swatsthe otherwise overpowered former protagonist Laharl. And during the final boss battle, she easily swats the entire party while musing about the constant pain and despair they (and their victims) have to endure when fighting endless hordes who only see a high-level achievement. The only way to defeat them in a straight fight is to be even worse than her, which unlocks an infamous Downer Ending where the player character goes insane from absorbing her power core and eats his siblings alive.
Judge Nemo in the fourth game shows how thoroughly humans rot everything around them and then some.
Barring a morbid Running Gag involving Void's secretaries, the villains in the fifth game are played surprisingly seriously, with very few comedic moments involving them. Until the post-game, where they start getting played for laughs.
Malice in Riviera: The Promised Land. Her first appearance is part of a very dark scenario, but the game returns to its lighthearted self when she leaves. Her return marks the shift of the game to its main themes and the serious core of the series.
The LEGO Adaptation Game series is a barrel of laughs and fun to play, although every now and then there is a villainous exception.
In LEGO Star Wars, the Emperor doesn't abide by this rule; he rarely has any funny scenes to show, minus one with his alter ego and he's more or less played seriously in comparison to the rest of the games.
LEGO Batman 3: Beyond Gotham has Brainiac. While not without his comical moments much in the way that Lex does, his introduction ends up shifting the genre from typical superhero/supervillain conflict to intergalactic crisis, overshadowing Lex and the Joker and shrinking the Earth. Moments where he mind-controls the heroes stand out as among the darkest in the entire franchise, in particular when he brainwashes Batman and nearly kills Robin, or when he enlarges and brainwashes Superman, very nearly crushing Batman onscreen. Aside from Brainiac, the level with Indigo-1 is among the darker moments of the campaign, since it shows her sociopathic nature when the HeelFace Brainwashing fails, and very heavily implies that she's murdered Abin Sur's daughter as in the comics.
Super Paper Mario has Dimentio. He starts off as exhibiting some humorous personality quirks, much like his fellow minions of Count Bleck. But as the plot progresses, he is revealed to be utterly psychotic, and quickly makes history by becoming the first villain to successfully kill Mario & Luigi (they get better though, as expected). This culminates in him stealing the Chaos Heart from Bleck and planning to remake the multiverse in his image once the old one has been destroyed, and then, when he is defeated, deciding to destroy it all anyway out of spite.
While Shin Megami Tensei is not a very lighthearted series of games to begin with, they all have their characters that really cause hell to start happening. For example, even when Alraune kidnapped men and a fellow Samurai in the beginning of Shin Megami Tensei IV, it was a bloodless event and nobody died. But shortly after, Kiccigiori burns and you encounter the Black Samurai. As soon as the Black Samurai appears, Mikado begins to crumble apart, 1500 Year old traditions are broken to capture the Black Samurai and this causes the old war of Law and Chaos to start up again.
Justice for All: Hello Matt Engarde. The Ace Attorney series will forever be comedic, and it seems to believe very much in well-earned happy endings, but Phoenix's first truly evil client gave it a definite darker twist that never really left. They also started the trend of having sociopathic villains as the Big Bad.
Dead Rising: All of the quirky humor from earlier in the game disappears completely as soon as Larry Chiang appears. His concept alone is one of the most horrifying concepts for the psychopaths in the game, the place you find him is dark and dreary (a far cry from the rest of the colorful mall), and his laughter is just unsettling. Oh yeah, he also is a cannibal who plans to shove Carlito Keyes into a meat grinder to serve to his "customers".
Shadow the Hedgehog's introduction into franchise took the series down a much darker and grimmer path. Sonic Adventure had a larger share of dark moments than any of the previous games but ultimately contained an upbeat tone. Sonic Adventure 2 (Shadow's debut) is certifiably a point at which the series started experimenting with much heavier themes and Shadow was certainly a catalyst in the series' move in that direction (which continued all the way up to Sonic Unleashed).
Black Doom from Shadow the Hedgehog is a pretty dark villain as well, having his aliens invade the world and planning to kill all humans (though he claims to only be trying to save them from a path of self-destruction). If Shadow chooses to help Black Doom in the Pure Dark path (and the player must view every ending in order to unlock the real ending) Black Doom has Shadow blow up a city with a bomb. Also, in the real ending of the game, Black Doom paralyzes Sonic, Tails, Knuckles, Amy, Rouge, and Eggman and tries to feed them to carnivorous aliens.
The Deadly Six in Sonic Lost World are an odd case: while they are somewhat goofy, hilarious, brightly colored characters, they prove to be some of the darkest villains in the series: upon betraying Eggman, they use one of his machines to drain the planet below of its energy (which is implied to be its life force) to make themselves stronger. Then, they plan to turn Sonic into a loyal robot, but due to a rescue by Tails, they capture him instead. Not that they don't try to turn him into a robot anyway, however, and after they have him, Sonic stops making fun of them and demands they give him back, unharmed. Eventually, Amy and Knuckles get their lives drained by the machine, and they (seemingly) manage to kill Eggman. It should be noted that this is the first time in the series where the events of the story actually manage to briefly break Sonic. Their appearance brought a sign that the wackier period of the series had finally started to wane.
Infinite from Sonic Forces is easily the most heinous character in the history of the franchise and definitely seems like a character from a grittier franchise. His dialogue is constantly peppered with death threats and he relishes in casually inflicting suffering on others; a Sadist to a tee. Even characters like Gerald Robotnik (who was driven to hatred by betrayal) and Black Doom (who is trying to usher in a new age) don't go to the depths of Infinite, who is only in the villain game to spread misery, wrath, and a sense of oppressive futility. He was a firm sign that the Lighter and Softer period of the series was officially over.
Chaos Lord Ledgermayne. Basically, many villains before it, especially some of the previous Chaos Lords, were lighthearted and comical in nature, and even mainly focused on Incredibly Lame Puns, big deal. Then cue the arrival of Ledgermayne, who proves to be almost invincible due to being immune to regular weapons and magics and even being able to control magic itself. And later, Ledgermayne reveals its plan to cut off all magic from Lore - all without caring about the fact that all life on Lore will die if it itself succeeds, which it is, of course, fully aware of.
Vordred, proves to be this as well. He shows players that he means business by using his signature spell, the Voiduminance Necrot-Morph, to turn other people, especially the very paladins he was trained to fight and destroy (after all, he is a Paladinslayer), into his undead slaves. And that's not all, his armor, which is made up of Too Many Skulls, is immune to light-based magic, and he gets even more powerful thanks to an experiment performed on him by ArcAttack with the help of the hero, plus he's the reason why Part 1 of the Doomwood saga is Darker and Edgier than the previous sagas in the game before it.
Bloodtusk Ravine's story proves to be the darkest out of all the Chaos Lord areas so far, seeing how Xing & Xang's scheme for the ravine is darker than their previous schemes were, and Krellenos also lands himself in this spot since he worked behind the scenes during the war between the Horcs and the Trolls and even murdered his own brother Antiphuus. Then Khasaanda kills and usurps her own twin brother, planning to use his powers to exact revenge on Drakath for what happened to her brothers themselves.
Sepulchure himself in the games made by Artix Entertainment that he appears in fits, seeing as how there's less humor when he's around. In contrast with many Harmless Villains working for him, he invokes fear in others and kills off many people, including the ones in the Guardian Tower he crashed his fortress into, as a show of proving that he means business. Of course, his lack of remorse in turning Fluffy into a Dracolich and causing death and destruction doesn't stop him from being an Anti-Villain with standards who loves his daughter Gravelyn so much that he becomes unwilling to kill her despite her being the Champion of Light he sought to destroy, and is trying to bring back his lost love Lynaria.
The series Big Bad, Dark Prince Satan, in the first arcade game. Whenever he appears in cutscenes, he's depicted in a barren wasteland with constant lightning striking, contrasting the typical field the other characters are in. The cutscene before you fight the Dark Prince takes it a step further, with ominous music and the Dark Prince swooping down from the shadows. Battling him also has a sense of tension, due to the more intense music that plays and the sound effects sounding like explosions. To top it off, throughout the whole game his normally goofy personality is downplayed, becoming The Comically Serious at best, due to Arle accidentally calling himSanta. The second game is the first one that depicts him as the Laughably EvilHarmless VillainFinal Boss he's better known as.
Satan becomes this again thanks toDoppelganger Arle in Puyo Puyo~n. While most end bosses in the series tend to fit the comedic tone of each game, Doppleganger Arles appearance and theme are much more serious and somber compared to the rest of the game, and her motivations (wanting to kill Arle out of pure jealousy) and actions (usingSatan's power to capture Carbuncle and lure Arle into a trap) were also taken more seriously as a result, being a stark contrast from what's a rather light-hearted series for much of its existence.
Rafisol from Puyo Puyo Chronicle is a notably big one from one of the SEGA-era titles, to the point where she could even go as far as to be considered the first true case of this in SEGA's run of the series. She's effectively a manifestation of hatred who only desires destruction, and if not stopped, could have destroyed Ally's world (with the implications that her destructive power could spread to other dimensions). But unlike Ecolo, this desire for destruction is played completely straight. On top of that, she's the only antagonist in the series that has assaulted another character during a cutscene. Becomes subverted in the post-game campaign though, with Character Development showing that she just wants to be loved by others.
The PC-98 release of Madou Monogatari 1 ends with a brawl against a disgusting-looking lich named Fudoushi, and when he presented that horrifying illusion of melting faces, you knew that this was definitely not going to be your lighthearted Puyo fare.
The Repliforce from Mega Man X4 effectively kickstarted the themes of how the term "Maverick" can be abused to truly horrific levels (though how much of it was earned due to the self-destructive idiocy of the Repliforce is up for debate), as well as showing a firsthand look at the tensions between Reploids and Humans, both of these themes playing a major role in future X games as well as being the main theme of the Zero and ZX series.
Theres also Doctor Doppler and the other infectees, who showed how powerful Sigma was and how his influence could spread into even innocent individuals like a plague, blurring the Maverick definition for the first time.
Mega Man Zero have Dr.Weil and Omega. While the Zero series was already the darkest of the franchise to begin with, Weil is far more of a menace than the villains of the first and second games. Zero 3 gets much darker with their appearance, the usual 8 bosses are now brainwashed by Weil and become downright evil, and he starts inflicting far more acts of evil than any Mega Man villain before him. And he is not misguided or a Well-Intentioned Extremist like Elpizo, is'nt evil because he put Reploids above humans like Sigma, or put human above Reploids like Copy X. He is a irredeemable, selfish monster who want humans and reploid to suffer under his rule.
Jasper Batt Jr. in No More Heroes 2: Desperate Struggle starts the game's Darker and Edgier tone off by the delivering the head of Travis' friend Bishop through his apartment window. There's also the revelation that all the CEOs of Pizza Butt Travis killed in the first game were all his family members, and he's merely perpetuating the Cycle of Revenge between the two of them. Once Travis actually meets him face-to-face, however, the game actively defies any attempt at serious drama by making him the single most ridiculous boss in both games, to the point that Henry even bails out after his Big Damn Heroes moment because the fight is just getting too silly for him.
Yuuki Terumi from the BlazBlue series. Though already pretty dark (even when compared to Guilty Gear, which itself was fairly dark compared to other fighting games to begin with), Calamity Trigger started off pretty light-hearted, with copious amounts of humor. Once Terumi revealed himself, however, everything gets dead serious. And it continues up until his near demise at Hakumen's hand in Chronophantasma. But when he survived in Central Fiction, he's still dangerous as ever.
Rosenkreuzstilette serves as a clone of and a tribute to the Mega Man franchise, with various nostalgic moments, some amounts of humor, a cast of cute girls, and an Affably EvilBig Bad. Then once Iris shows her true colors, things go south very quickly. You don't even have to go any further than the beginning of the side game Rosenkreuzstilette Grollschwert to see for yourself as she starts said story off by killing a random priest for the heck of it, and that's saying something.
Spyro the Dragon has its fair shares of loud villains who are evil but still have humour. That cannot be said for The Sorceress and The Sorcerer who are both no nonsense villains who have no regards for others. The Sorceress' plan was to kill 150 baby dragons for a spell to achieve immortality and The Sorcerer's plan was to drain everyone including children of their magic not caring if they're hurt and leaving them in an alternate reality.
Ghostbusters: The Video Game starts out with a lot of the same lighthearted humor of the film series, but things start to get considerably creepy when the Spider Witch turns up in the level where the Sedgewick Hotel is revisited. Like the other Node Guardians, she's murdered a lot of people, but we actually see the bodies of a lot of her victims and witness a reenactment of her leading one of her victims to his death. The lives taken by the previously encountered Node Guardians were at worst briefly mentioned, but actually knowing the full detail of the Spider Witch's crimes has quite a lasting effect on the tone of the game from then on.
The Flood are this in all Halo games they appear in. While the Covenant are indeed a serious threat, they at least have some charm and can be endearing and entertaining, particularly in their dialogue. The Flood, on the other hand, are Body HorrorNightmare Fuel through and through. Their appearance usually marks a shift from the games being full First-Person Shooters to semi-Survival Horror.
Scharlachrot from Arcana Heart 3 is the biggest one in the series so far. Not only does she have no comical moments, her introductions have her going berserk and trying to destroy all of Japan including herself. Even if you play her story route, where she is more mellow, she still has no comical moments.
Handsome Jack from Borderlands 2 was elevated from Obviously EvilJerkassIneffectual Sympathetic VillainLaughably Evil to this after he outright murders Blackwing, the Loyal Animal Companion of Mordecai, one of the heroes of the first Borderlands. The same mission also shows his horrific experiments against the people of Pandora, including Tiny Tina's parents. And then in the mission where you have to disable the power core, containing Jack's own daughter, Angel. Although it was done by the request of Angel itself, after the mission, Jack outright kill Roland, one of the heroes of the first Borderlands, captures Lilith to be used as replacement power core, and then loses many, if not all, comedic snarky moments in favor of angrily accusing the heroes as "child-killers" in a pure, unadulterated rage. And then all the DLC quests, which took place after Jack's death, were considerably Lighter and Softer and Denser and Wackier simply because the lack of Jack.
Queen Vanessa. A creepy spectre who only shows up in a single mission that briefly turns the game into an Amnesia-lite game of running and hiding from an implacable, invincible boss who turns anyone she can get her hands on into an ice statue. And while Hat Kid is hiding and Vanessa is hunting, the latter speaks to Hat Kid with the tone of a sweet grandmother asking her grandchildren to come play, with only subtelty of tone betraying the malice underneath. She's also responsible for the Snatcher — Vanessa was a complete Yandere who, falsely believing her husband was having an affair with a flower seller when he was buying Vanessa flowers, chained him in her basement until he died and became the Snatcher, which also cursed the once green land into the nightmarish Eldritch Location it is today.
The Empress, Arc Villain of the Nyakuza Metro DLC. Whereas the Mafia of Cooks was The Family for the Whole Family and utterly impotent, the Empress runs her criminal syndicate deadly straight, conscripting Hat Kid and forcing her to hand over any Time Pieces she gets, and has a Non-Standard Character Design much closer to something out of the Sly Cooper series than A Hat in Time. She's also seen calmly killing a subordinate who tries to steal from her, and in the end of the DLC, when Hat Kid steals the Time Pieces back, there isn't a Boss Battle — like Queen Vanessa, all Hat Kid can do is run and hide from an angry criminal kingpin with a rocket launcher while the entire Nyakuza chases Hat Kid down for a chance at the multi-million dollar reward on her head. And the Empress nearly succeeds, stopped from cornering and tearing apart Hat Kid only by the timely appearance of a pair of cops. Finally, if spoken to after the mission, while the police are investigating her jewelry store, the Empress makes it clear that it's only a matter of time before she makes another attempt to kill Hat Kid.
Final Fantasy V brings ExDeath. For a game that's lighthearted and at times outright silly, ExDeath's appearance serves to ram the severity of the world's problems into the heads of the characters. Most of the time when he shows up, the tone gets much darker and something in the world changes, usually for the worst.
Wadanohara has plenty of Arc Villains, with the game slowly becoming darker and the stakes being risen higher after each other. While Orca and Princess Tostasu were by no means pushovers and threatening, the game was still this adorable underwater adventure. This all changes when Sal reveals his true colors, shifting the game into a complete horror overhaul with plenty of Nightmare Fuel and Gorn cropping up. Sal himself is a loathsome villain, going as far as trying torape Wadanohara and tries to kill her and Samekichi when she rejects him.
Metroid is already a particularly dark series with its ominous atmosphere and alien abominations alike, but it doesn't give you much of a truly dangerous threat apart from boss battles. However, once Ridley appears, the lore not only takes a darker turn, but the tone of the gameplay switches from occasionally unnerving to utterly panic-inducing.
Street Fighter: M. Bisons debut in Street Fighter II began a period of more epic stakes and tone, with his machinations such as the Dolls and Psycho Power, along with him having killed Charlie. Akuma also qualifies, for introducing a more personal threat to Ryu, as both the source of the Satsui No Hadou and having (apparently) slain Gouken.
The fifth game of Princess Maker has several villains, from Big Bad, Co-Dragons and their assassins. First, you raise a 10 years old daughter as usual, but sets in modern Japan (a.k.a. your world) with peaceful and simple life, until the presence of Gateau, an assassin from rebel forces who has killed her biological parents and some princess candidates. The daughter gained her memory back after the incident (which was previously erased by Cube), knowing that she is originated from another world and now they attempted to kill her. The rebel forces wanted to kill all princess candidates because a princess has a special purpose: she keeps peace and harmony between 5 realms (Human Realm, Fairy Realm, Spirit Realm, Angel Realm / Heaven and Demon Realm / Hell) in her world, the rebel forces despise that.