24: Vladimir Bierko. Bierko's original plan was to assassinate the Russian president in the name of their separatist cause and attempt to blackmail President Logan into not opposing them. Once Logan didn't fulfill his end of the bargain, he switched into all out revenge on the U.S. and CTU, culminating in taking over a nuclear submarine with the purpose of destroying several cities, his original goal forgotten. The stupidest aspect of this is that his subordinate, Ivan Irwich, went through the exact same pattern earlier in the season (being focused on his goal to assassinate the Russian President, getting betrayed by the US then seeking petty revenge on the US). Then Bierko makes his on screen debut... and immediately kills Irwich for deviating from their goals, the exact same thing he would do two episodes later.
Alias: Irina Derevko was an unfortunate victim of this trope. In season two, when she was revealed as The Man, responsible for all the torture Sydney went through, it was explained away as Irina playing a role for Khasinau, who thought he was the real leader. Her betrayal of Jack Bristow was also subsequently explained as her being an unwilling pawn of the KGB, forced to marry an American agent to find out about Project Christmas and then fake her own death. During Sydney's missing two years, she and Jack team up to hunt for their daughter. When it becomes known that Irina has been doubled, and Jack shot the double, not the real Irina, she becomes a valuable asset to the CIA, and rather than let them take her back into custody, Jack lets her go. She repays him by helping deliver Sydney's daughter, even though she really has been trying to kill them both as part of her "plan". After all these shades of gray, she's revealed in the series finale as your stereotypical Card-Carrying Villain, wanting to kill Sydney and everyone else in existence in order to bring about Rambaldi's "endgame". She is given a Karmic Death, killed by Sydney as she tries to make her Great Escape before The End of the World as We Know It.
Babylon 5: The heroes defeat the Vorlons and the Shadows by forcing them to acknowledge their Motive Decay. The most damning thing that ultimately convinces them to leave the galaxy is that they don't have answers to their own Armor Piercing Questions anymore. The Vorlons no longer know who they are, and the Shadows don't know what they want.
Battlestar Galactica (1978): The episode Space Croppers begins with the Galactica's fleet being attacked by the Cylons. The Cylons destroy the fleet's food supplies. Boy genius Dr. Zee comes up with a plan to send Troy and Dillon down to Earth to get some supplies. Troy and Dillon pick a farm at random and soon find out that the farmer is having problems with the local growers' association. Instead of picking another farmer to get supplies from, the motive decays into helping this farmer out with his problems and the rest of the episode revolves more around helping a farmer than it does about getting food for Galactica.
Bones; recurring villain Christopher Pelant started out as a self-proclaimed "Hacktivist" whose grisly string of murders were supposed to have a political message. His most recent episodes have him concentrating on Booth and the Jeffersonian team (seeking revenge against Booth in particular, for severely scarring his face with a gunshot).
In Pelant's most recent and final appearance, Sweets determines that Pelant's ultimate end-game was nothing more than to seduce Brennan and drive her and Booth apart(explaining why Pelant forced Booth to break off their engagement in the Season 8 cliffhanger).
Breaking Bad: A major plot point. By season three Walter's entire motive to be a drug dealer is gone. His family has abandoned him, the money is no use for them, let alone for him to spend, but he likes it and is trying to rationalize what he is and what he has done. As of season 5, since Walt killed his boss, the main person threatening his family, and he has more money than his wife and son could spend in their lifetimes, the only thing putting everyone in danger is Walt not quitting while he's ahead. In the finale, he finally admits that his family was always just an excuse, and he did what he did because he liked it and because he's good at it.
Warren Mears was subjected to this in between seasons five and six. He built a subservient robot girlfriend because he was lonely, but found that he actually preferred a real-life girl who was his intellectual equal and "gave him a hard time". Xander even expressed sympathy for him (although he was undeniably a pervert). Yet by season six he's a full-out misogynist who Xander "could see as a Super Villain type."
The writers had originally planned to bring back Tucker Wells as the leader of the Trio. Notably, his troublemaking episode ("The Prom") was distinct from Warren and Jonathan's ("I Was Made to Love You" and "Superstar," respectively) in that it was intentionally malevolent as opposed to merely irresponsible. However, they couldn't get the actor. Ergo, Warren's "promotion" — and part of the story behind the gag of Andrew only being known as "Tucker's brother".
Faith is another example. In the heat of fighting, she mistakes a passing human for a vampire, and stakes him. What Measure Is a Non-Human? is a big deal to Buffy & co, because they really freak out about this. When it transpires that he was connected with the Mayor, she argues that killing him wasn't that bad because he was a bad guy anyway. Only the audience, not the other characters, are shown how upset she actually is by the incident. Then, within a short time, she's working for the Mayor, and the reason for her switching from his enemy to his Number Two is never really explained beyond 'she's evil now'.
Faith's slide from the heroes who excluded and distrusted her to the villains who appreciated her was clearly marked and a matter of Character Development. But after being very clearly conflicted, she switches to acting like she was completely evil all along, and the 'good guys' treat her as if that were true.
Criminal Minds: It's not so much that his motive got decayed, more like retconned, but the Serial Killer known as the Fox had something like this happen to him when he was brought back in the season five episode "Outfoxed". His crimes as revealed in his original appearance were breaking into the houses of families, then taking them all hostage and forcing them to treat him as the head of the household before eventually leading them down to the basement and killing them all, saving the father for last. In "Outfoxed" it was implied that he sexually abused the children he took hostage, and it was suggested that his crimes were essentially him lashing out at his abusive father and also at himself. In his first appearance, there had been no hint of a sexual component to his crimes and the reason given for his behaviour was that his wife and kids had left him and he was trying to recapture what it was like to have them, with him killing the families at the end because he knew the fantasy couldn't last.
Mandatory example: When they first appeared, the Cybermen, who at the time appeared roughly half-human, not mostly machine, had plausible motive for their villainy: they had become fixated with survival at all costs. By their fourth appearance the rails had begun to come off this idea and from then on, they've have various different motivations ascribed to them.
However this could be a Justified Trope as after the destruction of their planet and Cyber-Wars they needed more conversions.
There's also the Silurians, who in their first appearance were three-dimensional characters who had an equal claim as humans to live on Earth. Most of them wanted a peaceful solution to the issue, and it was just a few bad apples who led to it ending in tragedy. Their next appearance portrayed the entire race as genocidal maniacs. When a newly awakened subspecies of Silurians appeared in the new series some thirty years later, they shifted back to the original portrayal.
Has a positive example. Captain Crais's original motive for hunting down Crichton was to avenge the accidental death of his brother. This was something a simple discussion with Crichton could have cleared up, so the writers let them have that conversation, but in the context of a duel to the death that left Crais angry for a better reason: John won the fight and nearly killed him. Later, when Crais had more or less Heel Face Turned, he had another new motive for getting rid of Crichton: they were both in love with Aeryn.
Well, that and to get revenge on Scorpius who stole his ship, publicly shamed him, stole his life mission, and forced him into being a fugitive of the Peacekeepers.
Also, Crais never tried to get rid of Crichton ( that was Talyn), specifically because Crais knew that he ever laid a finger on Crichton, Aeryn would never forgive him... and would probably kill him, too.
Game of Thrones: A big part of Cersei's character at the start was that she loved her children and wanted them on the throne but as they die one by one she decides to take the throne for herself and grows distant of Tommen as time goes on. It reaches the point where she's downright callous when she coldly orders Tommen's body burnt after his suicide.
Sue Sylvester initially hated the Glee club because it was taking funding away her cheerleading team, the Cheerios. It later becomes clear that the Cheerios have boosters who "write fat checks" which take care of most of their expenses, and it seems Sue's machinations to take down the Glee club come from either a personal vendetta against Will Schuester or just a perverse love for stirring up conflict.
It was always more of "principle of the matter" kind of thing. Before the Glee club, the Cheerios were the only shining light in a highschool of mediocrity; the football team hasn't won a game in years, most everyone grows to get a job and live in the same town, and by being the best of the worst, the cheerleading squad dominated. And Sue liked being on top, with all the control. Even in the first episode, Sue could see that the Glee club had potential, potential that would take the light away from her team (and her), so she did all she could to make it not happen.
Heroes: Sylar's motivation has gone from "I want to be special" (first series) to "I have an uncontrollable Hunger which makes me lust after killing to get people's abilities" (second). By the third, though, he seemed to have decided that "this is just who I am and I'm happy with it." Now his aim seems to be simply Kill All Humans With Abilities - Danko points out that "if we succeed, you'll be the only one left", and Sylar just smiles and agrees. After, he want to be the President replacing the actual. In final season, he want to be a good person. Believing that, without his abilities, he would not be a monster, Sylar asks Matt to rid him of them.
Highway To Heaven: In the episode For the Love of Larry, a man and his boy are missing. Johnathan and Mark find the dog that was with them when they went missing. The Sheriff runs into Mark and Johnathan and shows them a picture of the missing man and boy with the dog. They explain that they found the dog, which is now in their rented cabin. Instead of asking them to take him to where they found the dog (as a good place to start looking for the missing man and boy), the sheriff asks them to take him to where the dog is now and when they find out the dog is missing, they start looking for the dog. The motive decay here is that they stop looking for a man and boy and start searching for the dog while two people are still missing. What was finding the dog going to do?
Kamen Rider Agito has the Lords, angelic beings who only target specific humans and for the most part, act as their protectors. Unfortunately, thanks in part to crossovers, their motives so decayed, that they even form alliances with (from extra-canonical history) their sworn enemy, the Grongi.
KARR. In "Trust Doesn't Rust", KARR's villainous acts are clearly the result of his childlike understanding of the world being misled by two petty thieves, combined with the Literal Genie aspect of his prime directive of self-preservation. When he reappears in "KITT vs KARR", he is simply evil, lusts for revenge against KITT, and seems unconcerned about his own survival. Neither Michael nor KITT find this odd, and the characters even know ahead of time that KARR is insane and out for revenge.
KARR always had an ego that KITT's existence threatened, and more importantly KITT had very clearly demonstrated himself to be a relentless and serious threat. Survival at all costs dictates a "either me or you" style vendetta to resolve the threat.
Could have been a result of damage done to KARR's circuitry either by the fall, by the ocean, or by "the mysterious benefactor who rebuilt him". It was shown a few times in the show that KITT was capable of being reprogrammed by turning a dial and messing around with the circuitry under his dashboard. KARR probably also suffered from this design flaw, but would kill anyone who tried to do so. It was mentioned that at least one person had died because of KARR, and that could well be the reason they died: they were trying to reprogram him. It was also shown that water in the various systems could disable them, and salt water is even less friendly to electronics.
In the episode, "Family Quarrel", Nels and Harriette Oleson have separated and Nels is living in the hotel. Doc Baker and Mr. Hanson get the idea that Mr. Hanson should go ask Harriette out on a date. The reasoning is that Nels will get jealous and will want Harriette back. In the next scene, Hanson is wearing a suit and carrying some flowers as he and Doc Baker walk toward the mercantile store. Doc Baker tells Hanson that now is a good time because Nels is out of town and won't find out. This subverts the original purpose, which was to make Nels jealous.
In the episode "Haunted House", Nellie and Willy dare Laura to go up to a haunted house. She runs away scared. Later, to redeem herself, she approaches the house again, but is discovered by the owner of the home. She ends up forming a friendship with the owner and never tries to prove her bravery again, even though it was an important plot point and her motivation for approaching the house in the first place.
Logan and Jessica in the TV series start out on a trip to find sanctuary. They say they're looking for it so they can go back and tell other people about it so they don't have to die on Last Day at Carousel. However, as soon as they're outside the city, they go on all kinds of adventures, sometimes abandoning common sense to allow these adventures to happen, like in one episode, they meet a man who says he'll take them to his city, but they have to abandon their vehicle and weapons. They gladly agree and trouble follows. The whole time they're looking for sanctuary, they could just go back and tell the people in the domed city that there's life outside and that it will be rough, but it beats dying at 30. Instead, they keep looking for sanctuary.
The same could be said for the sandmen who chase the runners. One of them is told by a council of old men that he can join the council and grow old like they have done. This is appealing to the sandman because he thought he would have to die at 30. When he gets outside the city, he should have had an epiphany, "Hey! It's not deadly out here. I could live past 30 out here, too! And others could join me!" Instead, he goes on trying to catch the runners.
Merlin: Morgana started season three as a vengeful young woman who was out to avenge her own people against the genocide King Uther had committed against those who used magic. Since finding out that Uther is her biological father she's moved from Well-Intentioned Extremist territory into flat-out evil, most recently manipulating her best friend's feelings for Prince Arthur (her own half brother who has never done anything to her) in order to try and assassinate her way to the throne of Camelot.
Lord Zedd and Rita Repulsa suffer from this. They go from wanting to conquer the Earth to wanting to destroy the Power Rangers, or even simply just ruining their day. Sure, if they get rid of the Rangers, they'll be free to rule the planet, but their plans noticeably go from "This plan will provide us with an unending power source or ultimate weapon that will allow us to take over the Earth" to "This plan will ruin Kimberly's chance at joining the Pan Global Games."
When Rita escaped her jar the second time, after being imprisoned in there due to Zedd taking over her Moon Base, she went from getting revenge on Zedd for imprisoning her via an overly complicated scheme involving marrying him to...just...sort of nagging him constantly due to his inability to kill the Power Rangers while she's just as unsuccessful at it herself.
Revolution: Charlie's search for Danny. She says she needs to get to him as soon as possible so as to avoid him being in danger too long, but sees it necessary to save literally every person they come across along the way who isn't with the militia, putting herself and her group in danger every time for people who they'll most likely never see again. This would be an In-Universe trope, but, over time, the rest of the cast doesn't even call her out on it. Episode 2 had Charlie saving people's lives. Episode 3 had Charlie help out a group of rebels. Episode 7 had Charlie save a group of kids, and the funny thing was that Miles wanted to get involved in that one. Rendered moot as of episode 10, due to Team Matheson rescuing Danny. Episode 11 ends with Danny getting killed off, meaning that there's no more motive to decay at that point.
The entire main cast suffers from this in Season 2. In Season 1, the main characters seemed to at least have a vague goal of helping the Rebellion, but as of Season 2 their only goal is to stop President Davis (before President Davis is even shown to do anything evil, all the characters already hated his faction)...but don't seem to have any identifiable goals beyond that. Are they still trying to restore the United States, just not with Davis in charge? Are they content to let the country collapse back into anarchy and feudalism after Davis is stopped? Something else entirely? Or is there no game plan at all?
The Borg had a small dose of this. Their goal started off as conquering and gaining knowledge. If possible, they would steal technology (most weapons don't work on them or they adapt) and just leave after maybe screwing the other side over a little bit more. Many times they would just destroy enemy ships. They would absorb a being of another species only when they needed information that you couldn't get from a computer (or they needed an ambassador). Come Voyager and the Borg seemed to have "adapted" and are now simply trying to absorb every species, conquering the universe, and stealing technology with absorbing species as the priority instead of as an afterthought.
Although their methods have changed their motivations are actually expanded upon starting in First Contact (and even sort of mentioned in The Best of Both Worlds) - they are pursuing perfection and harmony, to the logical extreme of their view.
The Tomorrow People: Jedekiah. In "Break Out", the shapeshifting android was not really villainous, but was perpetrating his apparently-evil deeds because he was under orders from a kind alien who mistakenly believed humans to be dangerous and barbaric. In his various reappearances, Jedekiah is simply evil, and obsessed with revenge, conquest, and the eradication of homo superior — and the Tomorrow People already seem to know this to be his natural personality ahead of time.
V (1983): In the original series, which followed the mini-series and The Final Battle, the visitors seem to have abandoned their original plan to steal all of Earth's water and use the people for food and have instead chosen to enslave the people for some reason. Even though they still use people for food, this appears to be a secondary motive rather than the primary purpose as it was in the original miniseries.
The Wild Wild West: In his earliest appearances, Dr. Miguelito Loveless was depicted as a Well-Intentioned Extremist, who just wanted to regain part of California, which was stolen from his ancestors (although he was willing to kill over a hundred people to do so) and share his inventions with the world. By the second season, he had become a garden variety Mad Scientist whose schemes revolved around either conquering the United States or the world, sometimes or getting revenge on James West.
The X-Files: The original motivation of Fox Mulder was to find his abducted sister. This actually weaves in and out of the story for a good four years, but then it's dropped nearly entirely. When he does find her, it turns out she was killed, not abducted, and is a ghost child running around a field. What should have been the ultimate climax of the story arc becomes a little sidenote a few years before the series actually ends.