In Spider-Man: The Animated Series, J. Jonah Jameson has a perfectly understandable and sympathetic reason for distrusting Spider-Man: his wife was killed by a masked assassin working for a mobster Jameson was about to expose, prompting him to start a crusade against people who wear masks and act above the law. However, in Mysterio's introductory episode, Mysterio, who has done next to nothing to earn anyone's trust and wears a mask himself, publicly announces that he's going to bring down Spider-Man... and is promptly lauded as a hero by Jameson. He's the one responsible for creating The Scorpion, although he does regret it later.
Vlad in Danny Phantom starts out with a rather sympathetic backstory and an almost understandable motivation: Jack, through sheer idiocy, caused an accident that sent Vlad to the hospital for years, costing Vlad's chance at Maddie, who ended up marrying Jack. Later episodes started ignoring it; in an episode where Danny changes history to prevent Vlad's accident (giving him absolutely no motivation for turning evil), he still turns out evil for no apparent reason. One could argue it's really a matter of personality in that Vlad has an unhealthy means of obsession despite different time periods. It's implied Maddie still loves Jack (Past Maddie is giving loving eyes towards Jack) in the altered timeline while Vlad is hinted to be bitter even during his college years (he crosses his arms in frustration when Maddie doesn't pay attention to him). With Jack alive, it's motivation enough for Vlad to go completely apeshit to preserve his happy ending. In The Ultimate Enemy, Vlad is shown as actually being a rather caring individual (willing to adopt Danny after he's orphaned, and willing to help rid him of his human sorrow for what appears to be purely altruistic reasons). So make of him what you will. His motives still decay over time, with less and less focus being on killing Jack and taking Maddie/Danny as his wife/son and more and more on just screwing with Danny and being his antagonist. At first he was an antagonistic in a half "I'll train you" kind of way and in the end he just went straight villain.
It seems to be more an inherent character trait. When he gets what he wants he's actualy a rather good and kind guy. It's just that when he doesn't he's quick to turn to bitterness and hatred to TAKE what he wants. The longer he stews the more unhinged he gets (to the point of making holographic and cloned copies of Maddie/Danny to try to have those when it's clear he can't get the originals). Going with the above, in the altered timeline he's rather normal and pleasant having both a fortune and the love of his life. But the moment he suspects things aren't quite going just his way he's quick to snap at people. It's just that in the main timeline he never had Maddie so he's basically stuck in villain mode most of the time.
Another addition to that is that Vlad gets so obsessed that he loses sight of the clear goal. At any point, Vlad could turn ghost and straight up murder Jack, but he doesn't. He pines after Maddie even with Jack there. Some part of him believes that he is a monster and he is Affably Evil most of the time. He isn't above begging and poisoning Danny's friends to get his help when he's dying, but he seems willing to be altruistic in certain situations. In The Ultimate Enemy, Vlad loses his former best friend and his long-time love of his life and has their son, an orphaned Danny, show up at his door. Given that he wanted a child of his own and just got a HUGE slap in the face by fate by the deaths, it is arguable that his obsession and priority's imploded and died. The last nail in the coffin was having Ghost Danny suck out his ghost form, combine with it, and straight up murder Human Danny without a second thought. That would have destroyed his mind (Vlad never killed anyone himself and seeing someone die by his actions would leave him forever guilty). He hated his ghost, but he missed it when it was gone. So to sum this up, his ex-best-friend, the love of his life, and their son/his adopted son are all killed and he lost his powers, his abilities to fight, and got to watch the whole world burn to ashes due to his mistakes. That...changes a man.
The Floaty Heads in The Secret Show parody this. Every single time they show up they want something different. It's not commented on in the show, but it is on the show's website.
An in universe example would be Hiroshi Sato from The Legend of Korra. Hiroshi joins the Equalists because a group of firebending criminals killed his wife. He screams this at his daughter during a fight. Asami retorts that he doesn't even love his wife any more, all he has is hatred. Hiroshi then moves to do what looks like killing his own daughter.
Macbeth from Gargoyles was an odd case - he only attacked the Gargoyles in his first appearance in an attempt to draw out the villainess Demona. By the end of that episode, the heroes had explained that she hated them too, which gave him no real motive to oppose them... yet every subsequent appearance found some excuse to feature him as an antagonist. First he went after a set of magical scrolls (that turned out to be diaries) that the Gargs had anticipated Xanatos would try to steal. Not once, but twice, he fought them under the Weird Sisters' mind-control — with a third incident that turned out to be a decoy robot double built by Xanatos. In a World Tour appearance, they crossed paths without trading blows, parting on fairly amiable terms, but then he was opposing their friend King Arthur in an attempt to recover Excalibur. For two full seasons, he was a recurring villain, who never once had so much of an Enemy Mine, despite having no specific reason to oppose the heroes.
After their cover was blown world-wide, he did get a cameo as a TV correspondent promoting friendly human-gargoyle relations — kind of funny since the experiences he'd had that were shown to the audience were almost overwhelmingly negative! But he doesn't hold Demona against the gargs as a whole. In the comic continuation he's becoming more of an ally.
Villains in Gargoyles tend to be more complex than your standard "tie the girl to the railroad track" fare. After the "City of Stone" arc, Macbeth's only appearances as a true villain were under mind control. He actually did have a valid reason to at least try to obtain Excalibur- he fit the prophecy as well as Arthur Pendragon did. And the episode during the world tour would count as a non-antagonistic appearance of the character.
Also, when he went after the scrolls it was because he believed them to be magical. He was probably going to use said magic to kill Demona (or himself since that was what he really wanted). He was only fighting the Gargoyles because they were in the way. Once he learns that that scrolls were diaries, he promptly gave them to the Gargoyles and let them leave.
Most villains in Batman: The Animated Series, and to an extent the comics, had genuine motives in their debut appearances, but the motivations for their later crimes was mostly "revenge on Batman"; to their defense, most of them were crazy.
Averted by the Scarecrow, who was always trying to carry out some twisted science experiment with the people of Gotham as his guinea pigs. When he did commit robbery and fraud, it was typically to obtain money to buy more chemicals.
The worst example is probably Clayface, who started out with the goal of getting revenge on Roland Daggett for causing his transformation, and in his second appearance was motivated by trying to get back to normal, both of which are sympathetic motivations that make perfect sense. In The New Batman Adventures, however, he had also become a petty thief.
He returned in Justice League however and only joined Grodd's group because Grodd promised him a cure.
Averted with the Clock King: In The Clock King, his motivation was simple: to make Mayor Hill look inefficient, and then kill him. In Time out of Joint, he still wants to do that (and destroy the new Judicial building). In the Justice League episode Task Force X, he works as a Boxed Crook, presumably to get on parole. And in a case of All There in the Manual, The Batman Adventures shows him successfully rigging the mayoral election so that Hill would lose. Batman is no more than a nuisance to him.
Based on the episode Trial, an argument could be made that the Motive Decay was intentional, and was being used to support a major theme of the show: despite all attempts at a Freudian Excuse, these villains were simply terrible people who, under one gimmick or another, would be causing misery and suffering to others no matter what.
Justified with the Batman Beyond villain Shriek, whose motivation did indeed shift from "commit murder at Derek Powers' request so I can keep my job" to "get revenge on Batman", but it's understandable because Batman made him go deaf.
Kim Possible: "Mathter and Fervent" presented us with The Mathter; he began by terrorizing Go City with vaporizing weapons because he was refused funding for his "unethical mathematical experiments". But after Kim and Hego beat up his flabby henchmen, he decides to make Ron (who has done nothing whatsoever at this point) his personal archenemy for no apparent reason in less than two minutes after they first meet. That's got to be some sort of record. He even goes to the extreme of erasing Ron's existence from all the computer records and then tries to off Ron in person for good measure resulting in Ron being zapped with a ray that turns him into an "Anti-Matter Boy" who disintegrates anything he touches. Wow. Talk about Disproportionate Retribution.
Almost every episode that involved any of Team Go, and especially when in their own city, tended to fall hard into superhero world cliches. Just as Kim Possible was a show lampooning the spy genre, they had their own fun with the superhero ones with Team Go. Example, Kim and Ron pick out Hego as the manager of the Bueno Nacho within minutes (his Clark Kenting was weak). Having taken Ron as his arch was simply "how it's done, who am I to argue" and between the choice of Kim Possible, the super strong Hego, and the pathetic sidekick, who would you want to choose as your enemy?
Now admittedly Teen Titans was never the greatest at establishing concrete motives for its villains (with a few exceptions), but a particularly solid case of decay still exists in the form of Brother Blood. He starts out as your typical power-mad supervillain pimp, helped by the fact that he has psychic powers, but then degenerates into wiping-out-a-city-For the Evulz territory and his final Evil Plan involves—becoming exactly like Cyborg. Why? Because he's decided that Cyborg is simply the greatest thing since sliced bread, apparently, which winds up making Blood look rather pathetic.
He does explain it quite clearly. He's obsessed with having complete control over his students with his psychic powers. Even though some like Bumble Bee could resist him, they could still be over powered if he directed his attention to them. Cyborg was the only person he'd ever met that was completely immune to his control so as his arc went on he became more and more obsessed finding out what made Cyborg immune and making more cyborgs was just semi coincidental with the fact you can program totally obedient robots and he already had Cyborg's blueprints so why not? The obsession with control is also intended to make him look pathetic as he keeps losing his calm demeanor when he raves about Cyborg's resistance.
Darkwing Duck averts this with most of its cartoonish super villains, but with Bushroot it follows this trope to hilt. Bushroot started his life of villainy to get revenge on the scientists who mocked him and destroyed his inventions and any chance with the woman he longed for. Some of his solo acts are committed in-line with his misunderstood lonely madman personality, such as trying to create sapient plants, but others are just plain supervillainy, like growing money to steal more money. Whenever he's teamed up with the Fiendish Five, or just partnering with another villain, any good side goes away completely. Quackerjack, on a lower level, switches from trying to rebuild his toy empire/getting revenge on the toys/businesses who drove him out of business, to just wanting to commit random acts of crime. Then again, he's insane.
The "growing money to steal more" plot of Bushroot's does still kind of fit with his misunderstood lonely madman motif, as he was using the money mostly to buy things for his plant friends.
Gargamel originally wanted to use The Smurfs to make gold (he's a capitalist after all) or capture them to finally get some respect in his life, as the Smurfs are thought by many to be mythical. For some reason, in later seasons, he simply wanted to capture/eat/destroy the blue communists for no real reason other than they kept besting his last plan to get them. This was made fun of in Robot Chicken where he said he never was clear on his motive.
One episode of the actual series infamously lampshaded it with Gargamel saying "I don't want to eat them, I don't want to turn them into gold, all I want now is to DESTROY THEM!"
In ReBoot Megabyte went from conquest of Mainframe to personal revenge in season 4. He even admits it during a monologue right before the cliffhanger.
You're probably looking forward to one of my erudite speeches about me, Megaframe, the new viral dawn, et cetera et cetera. But I'm afraid I'm going to have to disappoint you. There is no grand scheme here. This is about revenge.
At first, it seems Wile E. Coyote of Looney Tunes wants to eat the Roadrunner. Typical predator/prey relationship. But, some of the things Wile E. plans (poisoning, exploding, etc.) would make the Roadrunner inedible had they worked. At some point, his motivation became making that one, single, bird, DEAD.
Chuck Jones would often quote George Santayana's definition of a fanatic - "someone who doubles his efforts while forgetting his aim" - in describing Wile E. and intentionally made most of the humor come from the fact that even though gravity is clearly against him at times, he never gets the message and gives up/chases some other animal.
On Pearlie, the titular fairy's evil cousin Saphira would frequently come up with schemes to undermine Pearlie's credibility and get her kicked out of the park (so she could take over). While this popped up occasionally as the series progressed, in later episodes her schemes were usually either attempting to show up/embarrass Pearlie, or get revenge on one of Pearlie's friends (usually Opal) for various trivial reasons
Comes into play with Gorath and the Glorft's motives in Megas XLR. The whole point with Gorath coming back into the past in the first place was so that he could retrieve Megas and go back to the future and finalize the conquest of humanity that had been mostly-achieved when he left, but he jumps very cleanly into motive decay in the season 1 finale, where he resolves to destroy the Earth in the past.
Commander: But if you do that, we won't be able to go back.
Gorath: Then we won't go back!
Baron Zemo from The Avengers: Earth's Mightiest Heroes initially strives to kill Captain America, then extract a Super Serum. This would not only help Zemo create powerful subordinates, but also cure him of Virus X, which deformed Zemo after Cap stopped him from using it as a weapon against the Allies. Then the Enchantress (falsely) offers to help him Take Over the World, so he and she go round up a supervillain team, and Virus X never receives another mention.
Kang the Conqueror comes to conquer 21st century Earth so he can prevent a disaster that will destroy the world, including the empire he rules during the 40th century. After the Avengers put him in jail, he remains imprisoned for 31 episodesnote 30 if you treat "The Kang Dynasty" and "New Avengers" as episodes #19 and #49, respectively, instead of #18 and #49, until the Council of Kangs helps him get rid of the Avengers. Kang proceeds to send troops from the 40th century to help him take over 21st century Earth. Fridge Logic says that since Kang has troops in the 40th century, the Earth-shattering disaster must have been successfully prevented, and he doesn't have much of a reason to take over the world of the past anymore.
On Superman: The Animated Series, Metallo had this happen to him. His origin episode that transformed him from John Corben into Metallo ended with his vendetta focused on Superman, but also on Luthor for transferring his mind into the strong-but-numb Metallo body. However, by his second appearance the "vengeance against Luthor" angle has been dropped entirely and in his fourth appearance he even gets a girlfriend, despite the fact that his inability to feel anything at all when kissing a woman was one of the things that originally drove him nuts. His original motive does return in the video game Superman: Shadow of Apokolips, which debuted in 2002. Recruited by a disguised Luthor and told to destroy Superman, Metallo defers and goes after Luthor himself.
In The Spectacular Spider-Man, Sandman, like the Shocker and Beetle examples in comics, makes sure not to fall into this. All he wants is to steal stuff and get rich, make his "big score," and makes this clear when offered the chance to get revenge against Spidey. In his final appearance, he gets pissed enough during combat to cause a lot more collateral damage than he intended, and when he realizes it, he helps Spider-Man rescue the civilians, saying he'd only been in the supervillain game for the bucks and never meant anything like that to happen.
Plankton from SpongeBob SquarePants started out wanting to steal the recipe to the Krabby Patty, but over time, his motivation has changed to where he is willing to do anything as long as it's evil.
Ben 10 villain Dr Animo was first introduced as a scientist whose motivation was stealing a prize that he thought he deserved. This is completely dropped in all his next appearances, where he is portrayed as a classic super-villain trying to either mutate or conquer the world (sometimes both).
Well, he wanted to get the trophy and sic a bunch of dinosaurs on Washington DC.
Inverted with Charmcaster, whose motivations in the original show didn't seem to go further than getting more power and rivalry with Gwen. Ben 10: Ultimate Alien fleshed out her motivations by giving her a Woobie, Destroyer of Worlds backstory and revealing she actually was looking for more power to overthrow the tyrant who took over her home dimension and resurrect her father. After she accomplished the former and the latter proved impossible, she stopped being a villain and started going toward True Neutral.
Some argue she still suffered it in two ways: first that if those were her motives all along, they seriously decayed when she started fixating more on getting revenge on Gwen prior to those motives being revealed, and secondly that resurrecting her father wasn't really foreshadowed at all back when freeing her home dimension was established as her motivation, so it being a driving force for her came out of left field.
Zombozo was originally portrayed as a Emotion Eater who fed on people's happiness. This is entirely dropped when he returns in Ultimate Alien, and replaced by him trying to take Revenge by Proxy on Ben, which to some extent made sense (after all, Ben did ruin his business in his first appearance). Comes Omniverse, he is introduced as robbing a brain bank for no apparent reason.
Albedo was initially introduced with the simple goal to get Ben's Omnitrix so he could use it to free himself from his Shape Shifter Mode Lock and get his original form back, and, while he was rather psychotic in his methods, it was made clear he had no real evil intentions beyond it (in on episode, he manages to temporarly get his original form back, and was ready to just leave Earth without any further fight). In Omniverse, he actually succeeds in his goal, and now focus on revenge, which is still a logical approach. But then he turns out to be trying to absorb Azmuth's intelligence to become the smartest being in the galaxy, even though a major part of his personnality was about trying to prove he was smarter than Azmuth already.
The Zeta Project: Krick, the bounty hunter from "Taffy Time". In that episode, he wanted to capture Zeta for the reward. His next appearance featured him chasing Zeta not for the reward (which he no longer cared about) but to exact vengeance for what happened to him in "Taffy Time".
Atomic Betty: In her first appearance, Iciclia's main goal was to steal enough montegoberries to keep looking Young and she was foiled. In her next appearances, she's only seen Young-looking and there's no mention of her dependancy anymore.
The Dai Li in Avatar: The Last Airbender were founded centuries ago by that time's Avatar to preserve the cultural heritage of the city of Ba Sing Se. However, by the time of the show, they've become a Secret Police led by an Evil Chancellor — brainwashing dissidents, holding all the true power in the city, and hiding from the king the fact that, you know, they've been at war with the Fire Nation for a century. Of course, they end up joining said enemy.
Dark Vegan of Johnny Test, in his first two appearances, was a Knight Templar trying to destroy the Earth in order to maintain the Utopia of his home planet, but since Viewers Are Morons and can't know who to root for without the verbal equivalent of a bright neon light pointing to it, he was changed to just another card-carryingGeneric Doomsday Villain obsessed with taking over the world and destroying Johnny for no real reason other than because Bad Is Good and Good Is Bad. Interestingly, this happened at the same time he was altered from a genuine threat to life on Earth to a Harmless Villain who spends most of his time eating toast.