You know how the story goes, right? The Big Bad meets The Baroness, The Baroness meets the Big Bad, their eyes meet, and horribly discordant music that sounds not unlike the screaming of tortured souls arise. It's black magic... a match made in hell!
Lord Worldbreaker and Lady Firestorm are, individually, serious threats to the heroes, but what happens if they're suddenly working intimately together? That's when it gets really dangerous. A pair of villains capable of channeling The Power of Love is enough to give even the most hardened group of heroes a serious challenge, and worse yet, seeing the villains in love may make them doubt their own motivations. Should one of the villains fall, the other one grieving over their fallen lover is quite likely to initialize an Alas, Poor Villain scenario, and maybe even a My God, What Have I Done?. Should another villain start messing with the happy couple, it's usually played as a Kick the Dog moment.
...of course, these people are villains, so you can never really be sure that one or both of them isn't just playing at being in love, in order to manipulate and use the other. If the love was genuine but unrequited, expect the one who genuinely loved to sacrifice their life to protect the other, only for the other to disdainfully ignore them as they lay dying, proclaiming that they're no longer useful. Usually this signals a crossing of the Moral Event Horizon.
If both were faking it, expect them to show theirtrue colors at the same time. Hilarity Ensues - and it's never mentioned ever again.
The most classic version of this trope occurs when two previously established antagonists suddenly take a newfound interest in each other, but it can also involve a newcomer falling for an established villain, or even a pair of villains who were, from the beginning, a 'villainous couple'. In the first-mentioned scenario, Enemy Mine may occur in order to match the united power of the couple - which can get particularly interesting if the 'bedfellow' is another villain, who is driven by jealousy...
May form a Big Bad Duumvirate.
Compare Villainous Friendship, when the two are truly friends with each other, but not in a romantic way. Contrast Minion Shipping (which involves minions instead of actual villains) and Mad Love (which is one-sided). Outlaw Couple is the petty crime version of this. In the case of fiction with multiple villains where taking two out of the equation would still leave a bunch of bad guys, if it's genuine on both sides this can be used as a prelude to a Heel-Face Turn or at the very least a "Get Out of Jail Free" Card. If the couple in question is heterosexual, expect the man to be the more important half of the couple, possibly making her more of a Dark Mistress.
Subtrope of Even Evil Has Loved Ones. Not to be confused with Awful Wedded Life, which describes the marriage itself to be terrible; not the couple in question.
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Anime and Manga
In Mai-HiME, Miyu and Alyssa make a nice couple - so loving towards each other that Mai at first has a hard time believing that they're actually villains. This plays with the trope heavily; it's not a sexual relationship, though it's definitely a loving one, Alyssa's a Tykebomb rather than a true villain, and Miyu simply believes in My Master, Right or Wrong.
In Death Note, there is Light and Misa. Just what the Anti-Villain needs: A Psycho Who Works for Free. Then there's Kiyomi Takada. She and Misa have a little subtext argument about who's really his lover. As Near said "Light is popular with the ladies."
In Rurouni Kenshin Shishio Makoto and Yumi have a bit of a subversion on this. Yumi legitimately loves Shishio... When Yumi throws herself between Shishio and Kenshin during their battle to beg them to stop for Shishio's health, Shishio uses it as an opportunistic attack to stab THROUGH her to wound Kenshin. This appalls the good guys and Kenshin is horrified. Shishio calmly tells them that they don't understand since he and Yumi knew this would happen, and Yumi declares that she's happy she could help Shishio fight for once since she always was pissed off for being a Neutral Female. He then holds and comforts her while she dies and begs him to not lose... because he really loved her too - just enough to use her. But it's all good, sort of: after he perishes, they meet up in the afterlife and plan to take over hell together. Along with Shishio's devoted Battle Butler; he lights up at the thought of going into Hell if it means serving his master.
Riful and Dauf in Claymore are this. While she constantly berates him and threatens to leave him, when push comes to shove it becomes clear that they do genuinely love one another. A side story reveals, at least for Dauf, it was Love at First Sight.
Flame of Recca has Mokuren and Mikoto. They're quite happy until she gets wounded and he decides to just kill her For the Evulz. She probably should have known better.
Code Geass gives us Emperor Charles vi Britannia and his not-so dead wife Lady Marianne who are very much partners and crime, in love with each other, and evil.
In Shigurui, there's Lady Iku with Seigen to whom she is completely devoted to. It is unclear how much Seigen cares about her, although he does treat her much better (ie. like an actual human being) unlike her previous lover Kogan.
Subverted in Fushigi Yuugi. Soi loves Nakago, but he doesn't seem to reciprocate (although he does use her Deus Sex Machina to heal, and generally treats her pretty nicely for a Big Bad of his caliber). However, Soi gets killed in battle, and Nakago carries her corpse around. Make of that what you will.
Barbara and Lotten, the two antagonists of the Crashtown Arc in Yu-Gi-Oh! 5Ds, and clearly two of the most vile villains in the series, only officially married in the dub version, but still two lovers who were unrepentantly evil. (In fact, there's some debate over which was worse among fans; Barbara seemed loyal to him, while he was willing to leave her to die at the end to save his own hide, but on the other hand, he was the only one she was loyal to, and was willing to betray anyone else to get what she wanted, using seduction and her beauty to do so.
In Kekkaishi, this is implied to be the relationship between Byaku and the Princess, given the fact that not only do the two of them seem to genuinely care about each other, but they seem to only care about themselves and each other.
While not married to each other, Doctor Strange villains Dormammu and his sister Umar, both major mystic threats join forces (their mystic power is shared between them) to take ultimate power in a Defenders miniseries. Dormammu spends most of the alliance seeking Umar's approval and Umar finds ways to torment Dormammu. All in all they bicker like a married couple.
Again in the Marvel Universe, the Absorbing Man and Titania were married. Absorbing Man left her because Titania couldn't let go of her fixation with She-Hulk.
Fantastic Four villains the Mole Man and Kala (both rulers of subterranean realms, incidentally) have had a relationship that has been rocky and tumulous. They have been married and divorced more than once, and Kala has betrayed him at least once. When last seen, they seemed to have reconciled, at least for now.
Even earlier, The DCU has the Sportsmaster and the Huntress/Tigress, two Golden Age villains revealed to have married when they returned in the 1960s.
They had a daughter, Artemis, who became the new Tigress and then hooked up with another villain, Icicle. Last we heard of them they had a daughter of their own.
Harley Quinn puts quite a lot of effort into persuading The Joker to enter into this joyous state, but has only gone so far as Mad Love, probably to the benefit of all concerned. She does have a semi-regular relationship with Poison Ivy, whenever Mr J throws her out/tries to kill her or one of them is captured, but it never lasts long due to Harley's obsession with the Joker and/or Ivy's absolute misanthropy.
Death Of The Family: Poison Ivy and Clayface are now husband and wife. This may seem odd, but it makes sense when one considers that she's a plant lady and he's a pile of clay (which is a part of the earth), and plants and earth go together just fine! it was a ploy for Ivy, to use Clayface as bait for some plan
From the always reliably warped Doom Patrol, we have a rare gay example: The Brain, a disembodied brain who occasionally has a robotic body, and his Dragon Monsieur Mallah, a hyperintelligent French Marxist gorilla.
In the Yank Wilson story in the first issue of Next Issue Special, Rajiv Bahdgi and his wife Berlin Holiday are... special. Bahdgi's villainous activities have become wild, unfocused, and more destructive than ever since his marriage. When Yank Wilson and his team are sent to apprehend him, we discover why: his overbearing wife has been driving him mad and he wants to be captured just so he can get away. Unfortunately for him, due to the heinous nature of his actions, the government has a special arrangement for him in Leavenworth: he and his wife will be sharing a cell. Cue Big "NO!".
In the Sonic The Hedgehog comics, there's Scourge and Fiona Fox. Fiona pulled a Face-Heel Turn to be with him, and when Scourge took over Anti-Mobius and made himself king, he made her his queen. They seem to actually care about each other, as several times they've both come to each other's aid when it would have been easier to abandon each other.
There's also the Iron Queen and King, who thankfully were just a marriage of political convenience. Though, the Queen did have a thing on the side with Snively, and each seemed to be using each other to advance their positions in Eggman's empire.
During Stilt-Man's funeral, it's revealed that he and Princess Python from the Circus of Crime had been married.
In Lois Mc Master Bujold's novel Mirror Dance, House Bharaputra is run by a married couple, Baron and Baronne Bharaputra, who appear devoted to each other. [[spoiler/Although in the Baronne's case, it's possible that she's just looking for the extended life in a cloned body that he offers.]]
"In the past few weeks, they'd managed to convince everyone that they were in fact a loving couple rather than two psychopaths hooking up for kicks. Although Light wasn't too sure about L, the detective still seemed suspicious and watched their every move. Although Beyond kept insisting L was just a peeper."
In Those Who Stand For Nothing Fall For Anything there's Light and L when the two are ("working") together. Also Light and Takada of the variety where both are faking it for personal gain, although it's suggested that Takada does carry some affection for Light. Ryuk and L have some of this going, too.
You could also say in a Ho Yay sense for Voldemort and Quirrell, especially since later in the play after Quirrell is sent to Azkaban Voldemort's idea of getting off with Bellatrix is to be behind someone's head and hang out. At the end of the play, he and Quirrel are reunited after Voldemort is reduced to just a bodyless soul again needing a host.
The Author: Then by the power invested in me by myself, I now pronounce you husband and wife. You may kiss the bride, though I would prefer if you didn't.
It's not unknown for the Grand Highblood and the Condesce of Homestuck to be portrayed this way. Hivefled uses Deliberate Values Dissonance to crank up the villainy; they're moirails, and so by the standards of their society are supposed to be Platonic Life Partners who prevent each other from becoming violent. Not only do they actually make each other much worse, they had children, with the intention of torturing and sacrificing them later.
In South Park Bigger Longer And Uncut,Satan is in a gay relationship with Saddam Hussein, though the later is negligent and at times verbally abusive while Satan is sort of a loser. By the end it's quite clear that Saddam's main concern is that the coming Apocalypse will allow him to get back to Earth and conquer it for himself; with some prompting from Kenny, Satan finally snaps and kills Saddam.
Film — Live Action
Chucky and Tiffany from the Child's Play movies are vicious murderers, but love each other... most of the time.
Sol and Viper, the fun-loving cannibal couple in Doomsday.
The Mummy Returns had Imhotep reunite with a reincarnated Anck Su Namun in an unhealthily undead version of Reincarnation Romance. By the movie's climax he's clinging for dear un-life on the lip of a gaping hole to the ancient Egyptian underworld as the Collapsing Lair falls around them and the hero couple. He extends his hands to her for help, and she... leaves. Imhotep turns to the O'Connell's (where Evie did help Rick up) and gives them a heartbreaking smile before letting go. Anck Su Namun got punk killed shortly afterwards.
Anck-Su-Namun is even worse in the Animated Adaptation. Which is saying something, considering the movie version threw venomous snakes at people. It's implied in the cartoon that Anck-Su-Namun was just in a relationship with Imhotep for chance at achieving power; after he goes through the trouble of resurrecting her, she abandons him the moment she gets her hands on the Artifact of Doomof the week. When they encounter each other again in the series finale, Imhotep is apparently over her, as he leaves her to rot in the Underworld in an And I Must Scream state.
In Foxy Brown, the main villain is Katherine Wall, who runs a combined call girl and drug empire. Steve Elias is The Dragon of the organization, but also her lover. Katherine seems quite passionate about him, while Steve seems to have a more pragmatic attitude and keeps flirting with the call girls.
Bibok and Calosta in Esther Friesner's Majyk By Design. On Orbix, Majyk is a psuedo-sentient tangible substance that actually provides the power behind spells. Our hero Kendar may have scads of Majyk, but the two of them together are positively dripping with it. Married wizards and sorcerers have a time getting divorced if their Majyk doesn't want to separate. This is taken care of during the final fight when Kendar's ex-wife pretends to have had an affair with Bibok. Calosta proceeds to turn him into a variety of amusing shapes until finally he's turned into a rat which Scandal, Kendar's talking cat, eats, thereby gaining his share. Calosta was winked out of existence by Kendar's Aunt Carageena (Or was it Glucosia?) when her Sacred Eye of Delbert paperweight slipped out of her hands and struck Calosta in the chest. They didn't realize that the paperweight was, in fact, the actual artifact.
Odiana and Aldrick in Codex Alera. One is an insane water witch, the other is a brutal mercenary. They are also absolutely devoted to each other and every scene of them being together is filled with such tenderness, love, and overt passion for each other that you could easily forget the horrible violence they are perfectly willing to inflict on anyone else.
Lucius Malfoy is a bigoted terrorist who uses his money and power to manipulate others, while his wife Narcissa is a just-as-bigoted snob; yet as the series goes on it becomes apparent that these two's love for each other (and their son Draco) is their strongest and most (well, only) redeeming quality; as Voldemort begins to show just how little he regards any of them, their love for each other over him results in the family's practical Heel-Face Turn.
Vernon and Petunia. They're selfish and abusive to Harry, yet they seem quite devoted to each other.
This is exactly what goes on between Voldemort and Bellatrix Lestrange...in the latter's twisted and hopeless dreams.
Dangerous Liaisons has as its protagonists the amoral and sociopathic duo of Valmont and Merteuil.
Poppy Z. Brite's novel Exquisite Corpse has a gay version of this trope. Andrew Compton and Jay Byrne are necrophiliac serial killers who scheme to murder and eat the secondary protagonist.
Caine and Diana from Gone, by Michael Grant. He's a megalomaniac, power-hungry sociopath. She's a deceptive, selfish, manipulative girl who has betrayed everyone at some point. And yet they're in love, prompting him to make a temporary Heel-Face Turn, help the heroes, and try to kill his former lieutenant, who had just given her a nearly fatal injury, all for a chance to save her life. By Plague, though, it's debatable whether they love each other, or ever did. Caine lies to Diana and uses her for sex, and she leaves his side the second she realizes she can't control him. There are, however, those who think their relationship is beautiful, so we'll just leave it at a "maybe".
Norman and Sandra Arminger from the Emberverse. He is ruthless, imaginative, and a powerful warrior; she is cool, brilliant and manipulative. Together they form and control the Portland Protective Association, a medieval recreation/protection racket that seizes control of a huge chunk of the Pacific Northwest after the Change destroys most modern technology.
Stirling likes this trope: his Nantucket trilogy features the appalling partnership of deranged sadist Alice Hong and her husband William Walker, a genocidal warlord.
Red Seas Under Red Skies has Requin and Selendri. He's the vicious head of a casino where anyone suspected of cheating is put to death; she's his Two-Faced top enforcer. They are both absolutely devoted to one another, to the point where Requin hideously burned his hands trying to scrape off the contact poison that led to Selendri's current condition, then did something unnameable to the man who took out the hit.
In Death series: This has happened a couple of times, like in Salvation in Death and New York to Dallas. However, in those cases, one of the couple is genuinely in love and the other has nothing but contempt for the other. The contemptuous one will murder the other one, thereby crossing the Moral Event Horizon...if s/he has not already done so!
Sisterhood Series by Fern Michaels: A number of stories has this going on between the bad guys, like in Lethal Justice, Vanishing Act, and Deadly Deals. However, the "love" between such couples is apparently not genuine, and they will inevitably turn on each other once the Vigilantes and Karma start closing in on them!
It was apparent from the start that Billy-Ray Sanguine from Skulduggery Pleasant has a twisted affection for Tanith Low but it was only when Tanith got a Remnant permanently bonded to her soul that she started reciprocating those feelings. What makes it even worse is that Tanith is not in full control of what she's doing and so there's some very rape-y overtones on top of that. Squick indeed.
In Those That Wake's sequel, Arielle and Roarke are close, and implied to be romantically linked.
In Lois Mc Master Bujold's novel, Mirror Dance, Baron and Baronne Bharaputra, the evil heads of House Bharaputra, appear devoted to each other.
Live Action TV
The Addams Family is more Affably Evil than outright villainous, but Moricia and Gomez's relationship could technically qualify as this. They are a very loving couple, and their show is one of the few sitcom-style series on TV without marital strife as a running gag.
Angelus and Darla. Once Darla teamed up with Angelus, the duo started traveling the world, often staying wherever a genocidal civil war was currently going on.
Likewise, Spike and Drusilla, who seemed to be genuinely in love, albeit still quite psychotic. Sad it didn't last through all of the seasons. Spike's later relationship with Harmony counts as this as well, though it rather notably doesn't really work quite so well and doesn't last nearly so long, for more than one reason.
Lindsey and Eve.
Harmony with Hamilton.
Vampire Willow with Vampire Xander.
Charmed: Quite literally, if someone wants to remain aligned with Evil in marriage. It must be performed with a Dark Priest, at night, in a cemetery.
Chinese Paladin: Used as a means of demonstrating The Power of Love, when the heroes find a snake and fox-demon couple preying on travelers. The snake-demon sacrifices his physical form to save his wife, who then pledges to devote herself solely to preserving his soul. Unfortunately, the hero doesn't know about that, and kills her too.
Criminal Minds: Anita and Roger Roycewood, the couple of child abductors and murderers.
Dexter: A couple show up as Victims of the Week, telling each other that they love each other even while Dexter is about to kill them for murdering several innocent immigrants.
House of Cards (UK): Francis Urquhart seems to have a genuinely loving and mutual relationship with his wife, to the point where she will allow and even suggest that he have affairs in order to gain someones trust. She knows all of his devious acts (including the murders) and they conspire and live together happily.
The New Statesman: Even though he's the protagonist, Alan B'Stard and his wife Sarah are both amoral and power-hungry enough to qualify for this trope. (They take the idea of a "love-hate" relationship to whole new levels...)
Nikita: It's eventually revealed that Amanda is in a secret alliance/relationship with Ari Tasarov; together, they plot against both the protagonists and their respective superiors, in order to gain more control and power for themselves. Even after their master plan fails and they're forced to go on the run, it's shown that they actually do truly care about each other. One could even argue that their relationship itself is an Evil Counterpart to the one between Nikita and Michael.
In Mighty Morphin' Power Rangers, Lord Zedd and Rita Repulsa actually went as far as subverting the inevitable failure of the Love Potion - and eventually getting married. Later it's revealed that Zedd loves Rita for real, when he is exposed to an antidote against the love potion. The behind-the-scenes reason for this Unholy Matrimony is that the Moral Guardians thought Zedd, acting as an evil overlord, was too scary for kids during his early run. Therefore the producers toned him down by making him part of a bickering married couple.
This is why Space Pirate Divatox wanted to release Maligore in the Power Rangers Turbo movie. She started having second thoughts after getting a good look at him, seeing that he is a berserk fire demon.
In Power Rangers Zeo there were two cases of villains who had been married before making their first appearance (in a way, considering that both couples were robots). King Mondo had Queen Machina as his royal consort, and likely had for a long time. Also, Mondo's firstborn (first-built?) son Prince Gasket had eloped with Princess Archerina, the daughter of Mondo's rival, at some point in the past, and the two later returned when Mondo was believed to be dead.
Revolution: As of episode 8, Major Tom Neville and his wife Julia are revealed to have this going on between them. Their love seems to be quite genuine, considering that they went to great lengths to save their son's life, and that Julia is urging Tom to kill off Monroe and take his place as head of the Monroe Republic. Episode 10 shows that Tom would surrender before he sacrifices Julia. Episode 13 has Tom fail a mission for Monroe, and so he personally hurries to Julia and has her pack up and flee the Monroe Republic with him.
Batiatus and Lucretia have a great and loving relationship, but are the Big Bad for the entire first season. Notably a lot of their scheming, both in "Blood and Sand" and the prequel "Gods of the Arena" is done for love of the other, and they seem to bring out the worst in each other.
While Glaber and Ilithyia have a rockier relationship, they are matched in ambition and scheming skills. By the end of Vengeance, in the episode "Monster" they reunite for evil and declare they are both monsters. To stress the point they proceed to have sex covered in the blood of Seppia, whose corpse is still floating in the pool next to them.
True Blood: Russell Edgington and Steve Newlin. Slow dancing to Katy Perry in a frat-house full of bodies they've fed and murdered, flirting while glamoring Jason into showing where the fairies and his sister are hidden, Russell kidnapping a small werewolf girl so Steve can have his "first pet"... It's cute, on a sociopathic level.
Neither Hades nor Persephone were really evil (despite popular belief), but both were feared by the ancient Greeks and were generally dark beings (yes, Persephone too, in her role as Queen of the Underworld). Their marriage may have been based on kidnapping at first, but if nothing else Hades was far more faithful than the average god.
From Warhammer, the vampire couple Vlad and Isabella von Carstein. After turning Isabella into a vampire he raised a giant army of the undead and they tried to conquer The Empire. As you do. When Vlad was slain Isabella committed suicide.
Vlad took Isabella as his bride to seize control of Sylvania. He fell in love with her afterward, while she was still human, and did everything he could to avoid turning her into a vampire. Then a plague hit Sylvania, the doctors couldn't do anything for Isabella when she caught it, and Vlad, out of options, gave her an Emergency Transformation. She took it amazingly well.
In gameplay, if you have both on the table and one of them is killed then the othergoes completely insane, picking up Hatred of the enemy army and Frenzy. Translation: the bereaved spouse charges directly at the enemy lines and tries to rip apart the bastards that killed their love with claws and fangs.
From Dungeons & Dragons, Count Strahd Von Zarovitch believes that every hundred years his old love interest from before becoming a vampire is reborn. Naturally, he tries to marry her every single time. (He will never succeed, however; a Domain of Ravenloft is an Ironic Hell for its ruler, and for Strahd, this is the exact reason why.)
Another famous example of this from Dungeons & Dragons (which ended badly) was the relationship between Mammon, the ruler of the third layer of Baator, and Princess Glasya, the daughter of Asmodeus. Glasya was his lover and consort, but after the failed mass coup called the Reckoning, Mammon proved to be a groveling coward before Asmodeus. As part of his punishment, Asmodeus forced him and Glasya to annul their marriage. Glasya has since become far more powerful and become ruler of the sixth layer, and her attitude towards him now is unknown; some believe that they have secretly renewed their relationship (despite the fact that Mammon has a new consort) while others believe she despises him now for failing to defend their love.
From Deadlands fluff, we have Miles and Mina Devlin, ruthless railroad barons, dark sorcerers, devoted spouses and loving parents. After Miles' assassination, things go downhill.
Mr. and Mrs. Mao Zedong are largely portrayed as a loving and romantic, if occasionallydisturbing couple. The song The Chairman Dances is dedicated to this trope.
Monsieur and Madame Thénardier in Les Misérables. Though how deep the love goes is questionable. "I used to dream that I would meet a prince- but God Almighty have ya seen what's happened since?!"
In Twelfth Night, Toby and Maria spend a lot of time together preparing Batman Gambits in order to make fools of others, and sure enough, at the end of the play we find out that they've eloped.
To confront and expose the Big Bad in Baldur's Gate, the characters first have to get an invitation to his inauguration ceromony in the Duke's Palace. They get one from the two assassins Slyth and Krystin who hang out in the Undercellar brothel before they get to kill the remaining dukes. These two seem quite crazy and nauseatingly in love, and manage to put up quite a fight when you encounter them for the first time.
In the sequel you can cause this. There is two characters talking about how their familes are driving them apart since they're a bad influence on each other. One of your options is to be a Love Freak and tell them that they should run off together. They thank you and tell you everything they do shall be in your name. Later you overhear a conversation about those two. Turns out they were an Outlaw Couple and are now robbing people in your name.
Subverted in World of Warcraft, where the quarreling demon couple in Acratraz lets the heroes attack them one at the time while the other provides snarky commentary.
Deathwing and Sintharia. However, they were only together because she was the only one of his consorts strong enough to survive the mating after his Face-Heel Turn. Also during the earliest days of the Cataclysm Beta there was datamined info that Deathwing was going to corrupt Alexstrasza the Life-Binder and together they would conquer the world.
King Ymiron and Queen Angerboda, the leaders of the villainous Vrykul.
Sally Whitemane and Renault Mograine, the overseers of the Scarlet Monastery. Which have a villainous Lady and Knight vibe going on about them. As of the fourth expansion, this evolved into an Alas, Poor Villain scenario. Mograine had been canonically killed by his father ghost as revenge for his betrayal and murder of him (long story). So Whitemane carries on as the leader of The Remnant of the (in)famous ScarletCrusade, this time with Commander Durand to replace Mograine for gameplay purposes. But what really sells it are Whitemane's Famous Last Words following her allegedly final defeat:
Malygos and Saragosa. Killing Saragosa and then taunting Malygos over Saragosa's corpse earned the red dragon Keristrasza a Fate Worse than Death at the hands of a berserk Aspect of Magic. And then death, too, in The Nexus.
Lady and Killer from Shadow Hearts: From the New World. Though whether the latter was actually in love or merely Mind Controlled is debatable.
If they had actually finished the second game, this would have been possible with whichever love interest you chose on the dark side path.
A possibility with Blackguard Aribeth and the player in the end of Neverwinter Nights Hordes of the Underdark; or if you pick the evil path in Neverwinter Nights 2 Mask of the Betrayer the player and Gann/Safiya (depending on gender).
In the Shadowlords mod series it's possible for an evil female character to slowly corrupt Nooble Unders, paladin-wannabe through the right dialogue choices, while the sequel series, Dreamcatcher, has the option of starting a rather interesting romance with him.
LeChuck tries to do this in Tales of Monkey Island Chapter 5: Rise of the Pirate God, using his Voodoo powers from La Esponja Grande and the Crossroads to turn Elaine into a Demon Bride/Goddess like himself which makes her turn evil. It's all a plan by Elaine, to allow Guybrush to save her and defeat LeChuck later.
Before that, it is discussed at the end of Chapter 4, when, after LeChuck breaks free from prison and saves Guybrush and Elaine after the cure of the Pox of LeChuck, he tells our hero that "it was the only way to win Elaine's hand in unholy matrimony"... getting him confused and allowing LeChuck to make a clever, fatal ambush on him.
Traffic Department 2192. Near the end of episode 3, Generals Talon and Marilith are not only lovers, but conspiring to murder the other generals, Kreel and Orlok, in contention for the position as the Overlord's successor.
Being made by BioWare - and a direct sequel to the Knights of the Old Republic games mentioned above - it comes as no surprise that the MMO Star Wars: The Old Republic has this. The main example is Darth Malgus, one of the main villains, who's happily married to a cute Twi'lek (ex-)slavegirl. The fact that he treats her like a wife rather than a slave is a source of annoyance to the largely xenophobic empire, but since he refuses to play politics and spends most of his time on the Imperial Fleet fighting (and mostly winning) battles for the Empire, it's largely ignored. That, however, does not mean that their apparently genuine, two-sided love doesn't wind up with a tragic ending...
It's also possible for a 'Darkside' player character to start a relationship like this, with an equally-evil companion. Perhaps the most poignant of these options is the Male Sith Warrior, who can corrupt the Jedi Padawan, Jaesa Wilsaam to the Dark Side, and take her as your apprentice - and later, lover. She even admits that, to her own disappointment, she can't live up to the true Sith Ideal, since that includes seeking to betray and murder your Master when you get the chance - and she can't do that since she's fallen for you. Awwww...
On the other hand, if you play your cards right, it's also quite possible for a Darkside player to start and maintain a relationship with a 'Lightside' companion, and acting genuinely carring towards him/her even as you slaughter innocents and inflict pain and misery left and right. Which creates a whole 'nother spin on this trope...
In Mileena's non-cannon ending of Mortal Kombat II, she is a "secret partner" with Baraka, they both kill Shao Kahn and takes over the Outland, ruling it as king and queen.
Interestingly, this is quite a divergence from the source material, in which Cao Pi amused himself with Zhenji for a while - after killing her first husband and basically taking her as spoils of war - and then forced her to commit suicide when he found a new favorite. Presumably, it was decided that this wouldn't play well with a contemporary audience.
Done very humorously at the end of Super Mario RPG. Booster proposes to Valentina in Marrymore, and she says "yes"; however, he chickens out for some unknown reason at the altar, causing her to chase him.
Sorceress Mortis and warlock Isa in the Spirits of Mystery series. Their affections were quite genuine, as shown in the bonus chapter of Spirits of Mystery 4: The Silver Arrow.
In Umineko no Naku Koro ni, it turns out this is the case between Bernkastel and Lambdadelta, who have similar circumstances and would both do anything to stave off boredom. The latter is rather Ambiguously Evil though.
Trudy: We both had this... appreciation for the sadistic and morbid. We enjoyed our evil pranks so much that we quickly fell deeply in love with each other. It was black magic.
Subverted in Episode Five of the webcomic Demonology 101, when Isaac, the main villain, and Madeline, his demon 'handler,' genuinely falls in love halfway through the episode. She was supposed to keep him out of trouble, but once she starts sympathizing with him, winds up encouraging him to kill his brother Gabe. (As if he needed more encouragement.) However, when she herself is fatally injured, Isaac willingly barters her cure for a final truce with Gabe and the other protagonists.
Riku: Well, my skull's caved in and I'm stuck in the ceiling. I think I popped some vertebrae too. Aerith: Well, pop 'em back in! You've got more slings to be shot out of! Axel: God I love you.
In Kevin & Kell, Angelique is accidentally set up with R.L. after someone hacked into the Flea Bay website for a grooming date. R.L. plans on eating Angelique at the end, but becomes enamored with her after hearing Angelique brag about cheating on Kevin during their marriage, and managing to get him to pay her alimony despite initiating the divorce. The two soon marry after Angelique gives R.L. secrets on catching rabbits. Even when R.L. was missing (presumed dead) and Angelique took over Herd Thinners, restructuring it and using it as a stepping stone to conquer the world, he wasn't bitter. He just pointed out what a headache world conquest was. Angelique agreed to just make loads of money instead. And when the two shared a prison cell, they were just happy to be together. The only thing they needed beyond each other to be happy was their kids.
Occurs between Mad Scientists Spencer Ecchs and Ada Byon in Patchwork Champions. She seduces him on the orders of another supervillain to steal his secrets, but when she carries out her mission successfully, the two continue to date, ending with her joining Ecchs's group and marrying him.
In Sluggy Freelance, it looked like Crushestro and Monicruel were heading this way, until Chestro, his real wife, arrived. If she's not eviler than them both, she's at least more wrathful, and knows how to hit a cheating husband where it hurts — his criminal conglomerate.
Nonetheless, Crushestro didn't waver - and, in fact, divorced his wife to stay together with Monicruel. They are adorable together. Or were, until Hereti-Corp attacked their secret base and hit Monicruel with a DFA. Crushtero survived - barely - and his reaction to seeing her apparently disintegrated certainly removed all doubt about HIS feelings, at the very least.
Some examples in the Whateley Universe, natch. Some of the Bad Seeds (a clique you can only join if at least one of your parents is a supervillain) go to Whateley Academy. Nephandus has as parents The Troll Bride and Hexmaster. In a slight subversion, they're regarded as the Battling Bickersons of the supervillain world.
In the Transformers Animated episode Society of Ultimate Villainy, a new villan shows up called Slo-Mo, who can slow things down. She apparently also can reverse aging, as she did with Nanosec. She and Nanosec flirt with each other throughout the episode. Swindle stealing Slo-Mo's timepiece (the source of her power) is a definite Kick the Dog for Swindle.
Slo-Mo: I like a man who does it fast.
Nanosec: I like a girl who takes it slow.
Interestingly, they subvert the gender dynamic mentioned at the top of the page: while they act as equals, Slo-Mo is far more important to the episode's plot.
In an episode of Kim Possible, Dr. Drakken manages to charm DNAmy into cooperating with him. While Amy seems remarkably responsive to his cheap pickup lines, the most interesting thing about this single-episode teamup is probably that Shego seemed to be downright jealous...
One episode of Care Bears had Professor Coldheart convince villainess Auntie Freeze he wanted to marry her, and asked the Care Bears for help throwing the wedding. The gullible Care Bears agreed, reasoning that anyone capable of Love can't be bad. The reason was to sneak in an organ loud enough to destroy the cloud kingdom and crash the bears down to Earth, but when Auntie figured out it was a sham, she just twisted his ear and led him off to receive punishment...
On Cyberchase, Hacker and Wicked have an on-again, off-again partnership. They seem to be genuinely attracted to each other, but they'll also stab each other in the back the moment they think they can get away with it.
An example of two villains who are a couple from the beginning is Boris and Natasha of Rocky and Bullwinkle.
Another one (which arguably fits the Happily Married Trope more than any other example on this list) is the Monarch and Dr. Girlfriend (pictured above) of The Venture Bros. (they get married at the end of the second season and become an officially licensed supervillain team at the start of the third season).
It's left kinda vague in the movie, but other story material later explained there was no romance involved from either side — Sidorak merely wanted to "marry" Roodaka because then he'd have gotten political influence over her island. Actually, since it's also been revealed that Sidorak's achievements were actually Roodaka's doings, and he only stole the credit from her, it's clear that both were seeing each other as mere tools. It's just that, again, the movie makes it look like he had the hots for her.
In El Tigre this happens between Puma Loco and Sartana of the Dead. It seems that both of them are faking it at first, but towards the end it is revealed that Puma Loco does holds a torch for Sartana. It gets a little Squicky as Puma is human while Sartana is a walking skeleton. Word of God says that they had a son together, though their relationship was on and off.
Destro and The Baroness from G.I. Joe. They had a rather established relationship by the third miniseries and in the comics, they had been together since before they joined COBRA. In the comics, whenever one has been in serious danger, you'd best be prepared to get out of the way of the other because they will stop at NOTHING to ensure each other's well being.
Mac and Molly Mange of SWAT Kats. They were powerful gangsters and married before they died the first time and when they came back as robots, they quickly cheered over their new strength, durability and firepower. Yeah, they bickered a lot, but when one of them got hurt, you can bet your aft that the other would drop everything to save them.
Chief from Pucca, head of the local Quirky Miniboss Squad, has a crush on Garu's enemy Tobe. In one episode they became this trope after Tobe got hit by one of Cupid's arrows, and they had a little love montage showing them robbing stores together and so on. In fact, before the stuff wore off they were this close to getting married (The trope name is even used).
Moral Orel: Clay and Ms. Censordoll, at first competing in office, end up making out with each other at the end of "Nesting." They share a mutual infatuation with eggs, the former due to his Oedipus Complex and the latter due to having been "castrated" as a child.