When Vegeta was first introduced, he wanted to use the Dragon Balls to wish for immortality and rule the universe after he killed Frieza for years of enslavement. Although he was upset with Goku for 'beating' him on Earth, fighting him wasn't his primary goal, seeing Goku as more as an annoyance or a pawn to his end goals. After Namek, Vegeta lost all desire to rule the universe and live forever. Instead, he becomes completely obsessed with surpassing Goku. Some of this could be motivated by the fact that it was Goku who beat and humiliated Frieza, while he, the Saiyan Prince, was given a dog's death and reduced to begging a lower class warrior to avenge him.
Frieza himself also undergoes this. When he first appeared, he, like so many before him, wanted to use the Dragon Balls to gain immortality and stay in control of the universe forever. After Goku defeated him on Namek, Frieza loses all desire for the Dragon Balls, instead becoming obsessed with getting revenge on Goku for his humiliation.
Magical Project S Pixy Misa starts every episode ruining the balance of good vs evil (that's her purpose) but ends acting for the Evulz and more often than not ends vacationing (justified in that she is not actually evil but she just represents the repressed aspects of Misao and doesn't really care for her goals) instead of torturing Sammy and in one episode she ended having vacations instead of destroying Sammy.
Also, Ash's goal was To Be a Master; that is, to become the world's greatest Pokémon Master (a Pokémon Master being a trainer who is an official part of the Pokémon League, though exactly how one achieves that was always vague). Nowadays, this goal is barely referenced, and Ash seems to be going around fighting Pokémon battles for the heck of it. In Season 9, he was even offered the position of Frontier Brain, which would probably make him a Pokémon Master, but he turned it down.
The Team Rocket trio, who originally decided to follow Ash because his Pikachu blew up a Pokémon Center. Since they were trying to steal strong Pokémon, this made sense. Through the show's run, however, we have encountered numerous Pokémon who are significantly more powerful than Pikachu. They continue (on and off) to attempt to get Pikachu because they refuse to give up, even though their boss never cared about Pikachu in the first place.
This sort of thing happened across international lines as part of 4Kids Entertainment's dub of Yu-Gi-Oh! They usually played down the sympathy-inducing backstories of the villains and made them more evil. Pegasus' goal was the same (to bring back his lover Cecilia) but the methods were more ruthless. In the original, he needed to defeat Yugi so that he could gain control of Kaibacorp's technology and create a hologram of Cecilia to live with. In the dub, he wanted Yugi's Millennium Puzzle and all Millennium Items so that he could bring Cecilia's soul back and infuse it into the hologram. It's said in the dub that in doing so, he could inadvertently destroy the world. Although probably unintentional, this motive shift actually makes sense in the long run, as the seven items together DO open the door to the afterlife (where Pegasus could get Cecilia's soul) and also unleash the power of Zorc Necrophades into the world, which could indeed destroy it against Pegasus's wishes (this is Yami Bakura's intentional goal.)
Marik/Malik got it worse, though. In the original, he simply wanted to escape the life of a tomb keeper, kill Yugi (more specifically, the pharaoh), whom he believed had killed his father, and live peacefully ever after with his sister and stepbrother. In the dub, this is changed to him wanting Yugi's Millennium Puzzle and the God Cards to rule the world "as pharaoh". It's even worse with Yami Marik, who, in the original, was essentially the Joker with ancient Egyptian shadow magic. In the dub, he wants to rule the world, too.
Meanwhile dark Bakura suffered this in-universe for a while, retroactively. He turns out to have had fairlygood reasons for messing with the royal family, at one point, which somehow became a plan to destroy either Egypt or the world, partly because the spirit of hatred born from the slaughter of his family (Japanese) or an ancient primal destructive dark thing (English) teamed up with him. He seems to have entered the series with amnesia, carrying him still farther from sanity. But he gets back to the revenge-and-end-of-world thing in the Millenium World arc.
Naraku from InuYasha has changed motives so many times that eventually he was evil just for the sake of being evil. Initially, he wanted to use the Shikon no Tama to become a powerful full-fledged youkai, so his goal is getting all the shards of the Jewel. But then, he was somewhat driven by his lust for Kikyo and hatred for Inuyasha, both coming from his human heart, so his goal becomes getting rid of that. He succeeds in separating his physical heart and discarding his feelings for Kikyou, so now his goal changes to killing her. But it turns out he needs both his heart and feelings to do this so the goal becomes reabsorbing them, and when he does, he finally kills her. In the end, he succeeds in getting the whole Shikon Jewel, but he neither absorbs it nor does he wish on it, he just decides to use it to kill his enemies. Naraku himself admits he's not sure what comes next after he's done that. Yes, that's right - he spends over 500 issues of the manga trying to get the jewel, and once he finally has it, he's not sure what to do with it. Even worse, it's revealed later that he did make a wish on the Jewel but was not granted: to have Kikyou's heart. However, Naraku is an amalgamation of many Youkai and a human man called Onigumo, so it's understandable that his personality traits and goals not only change significantly (it has even been a plot point on occasion), but also contradict each other; especially when it comes to Kikyou and the Jewel. The youkai hate Kikyou and want the Jewel to become powerful, but Onigumo "loves" Kikyou and wants the Jewel to have her.
Orochimaru's experiments and his usage of different bodies from ninja, started as a method to learn every jutsu and gain immortality. However, his continuous experiments in the Cursed Seal seem not to do that and turn them into monstrous beings, not really related to his original goal. Sasuke actually called him out on this before finishing him. Then it's later revealed that Orochimaru's original reason for wanting immortality was that he was heartbroken by his parents' deaths and wanted to make sure he'd still be around to meet their reincarnations no matter how long that took. As his immortality research took ever darker turns, he completely forgot about this.
Inverted with Sasuke. His goals have always remained more or less the same: kill his brother, Itachi, and restore his clan, but how he plans to accomplish these goals has begun to vary wildly as the deterioration of Sasuke's mental state has become more rapid. After Itachi's death, his goals switched from killing Konoha's elders, to killing Danzo, to destroying Konoha, to killing every last man, woman and child in Konoha because he believes they're laughing at him over the unprovoked destruction of his clan.
Jerid Messa from Mobile Suit Zeta Gundam starts off as an ambitious elite soldier (by mediocre Federation standards), and has the goal of one day leading the Titans forces, even if the only reason is for the power that such a position would provide. A number of situations in the series even make him a relatively good guy in everyday life. After one too many fights with the series protagonist, he has transformed into an individual completely focused on nothing but pure bloody vengeance.
To be fair, his breakdown is largely precipitated by the death of his love interest Maua Pharaoh. Who was one of the more decent characters in the series. While she's on the "bad guys'" side, she's never shown to do anything morally reprehensible herself, which is saying something in a series where even a good number of the "good guys" are former nazi-expys with questionable motives and war crimes on their rap sheets. It's also entirely possible that he believes his original goal of leading the Titans will never come true if Kamille keeps standing in his way.
Same for Mashymere Cello in Gundam ZZ. Captain of a Neo Zeon ship, very idealistic and unwilling to authorize actions that would endanger civilians. Tries to keep his cool and conduct battles in a way that would make Haman Karn proud of him. Ducks out early on after it's decided he's not up to the task of defeating the hero... only to come back later on as a cold and merciless soldier. In an aversion though, the final battle still shows him as the lesser of two evils due to an Enemy Civil War, and he gets to go out in a blaze of glory.
This is a side effect of having even more CyberNewtype enhancements. Best case scenario, the enhanced person goes a little nutty. Worse case scenario, they become raving lunatics bent on causing as much property damage as possible. Mashimar tends toward the latter.
Blue Cosmos from Mobile Suit Gundam SEED suffers greatly from this trope. Originally they were an environmental pressure group, but after Human genetic enhancement became possible they shifted their focus to preventing widespread genetic modification. After genetic enhancement did become widespread they became a militant/terrorist organization bent on killing anyone who had their DNA altered. When war finally breaks out between the genetically enhanced Coordinators and the natural humans of Earth Blue Cosmos begins artificially enhancing their own people to fight one on one with the Coordinators (because apparently it's okay if the enhancements are based on cybernetics and addictive drugs rather than genetic modification). Then it all turns out they were just a catspaw to Logos who do it for profit.
Suzaku Kururugi in Code Geass starts off as a heroic upstanding fellow, who wants to change the system from the inside. After the death of Euphemia at the hands of Lelouch, he more or less seems to go temporarily insane, leading to a justified battle with the Magnificent Bastard Protagonist Lelouch. However, in the interim between both seasons going well into R2, not only has he become a Jerkass of ridiculous proportions, he has sold out his old best friend for a step up the power ladder, and his goal of changing the system from within has degraded to making his own homeland a better place (effectively giving the rest of the enslaved Areas of Britannia the middle finger). He does eventually realize that prioritizing means over ends really doesn't pay off after a couple of My God, What Have I Done? moments and proceeds to team up with Lelouch to save the world and atone for his sins.
The Black Knights undergo a similar one in R2 19 when they intend to sell out Lelouch to Schneizel in exchange for Japan, at the expense the rest of the world represented by UFN, for which the B Ks made up the primary military force, and their fight against Britannia's dominion of the world, and there was no actual guarantee that Britannia would keep their hands off of Japan once and for all. (And their own ally Kallen was nearly caught in the crossfire.) None of this went very far at all, given that Lelouch was whisked away by Rolo in a Heroic Sacrifice the moment things started to go south, and Xingke and Kaguya would soon catch Ohgi trying to cover the whole thing up.
After the aforementioned event in addition to Nunnally's apparent demise, Lelouch, who prior to the betrayal had actually assembled a legitimate front in the UFN to battle Britannia, now decides to go it alone, abandoning all personal inhibitions and willing to use his geass on anyone and go to even more drastic extremes, including making FacelessSlave Mooks out of his new army, detonating the world's biggest energy reserve and apparently causing more death and destruction than he did during his rebellion pre-betrayal. The latter (or former technically) was at least somewhat justified because of the opposition he faced off against. It's not that he became evil per se; the plot justifies it as him centering the world's hate around him for world peace. However, given the leading circumstances and the plausibility of such a plan (and Lelouch's own admission that it was a gamble), it all seemed like a convenient death wish for him. The aforementioned fact that causing worse, unnecessary destruction was a path to atonement, even as a mask, when it is even noted in side materials by Lelouch that there are other methods, makes it seem more a case of Designated than Necessarily Evil.
Charles being a Well-Intentioned Extremist reveals him to be worse than Lelouch and Suzaku combined in this regard. He conquered most of the world just to take control of the Thought Elevators scattered around the globe, allowing him to get to the World of C to destroy "God" and kill free will itself.
Asuham Boone in Overman King Gainer wants revenge on Gain for his sister, but is an overall good guy. Eventually his obsession as Gain continues leading the Yapan people to Yapan leads him to decide to freeze the world using the Overdevil. Its eventually revealed that Asuham's sister had a one night stand and Asuham overreacted.
Roy Mustang starts out trying to become the best damn leader in the world, but it starts to go wrong when he faces Envy, who killed Hughes. Fortunately, Hawkeye helps him out. With death threats.
A better example would be the Big Bad — he originally started out as a lab experiment who couldn't survive outside of the tiny flask it was created in, and caused the end of an ancient civilization to gain a human body of its own. After that, it starts an elaborate Ancient Conspiracy, sealing itself in a dark underground hideout, preparing for the day it can absorb God. Van Hohenheim even points out that it's essentially back where it started.
Haru, The Hero of Rave Master, had a pretty easy motive "I want to save the world". He keeps it up for all 35 volumes. It's the Big Bad, Lucia, who can't seem to decide what his reason for fighting is (lampshaded once). When he first appears he claims to simply be after power, then he wants to prove his family isn't crazy (by taking over the world), then he wants to be a god, then he wants power again, then he wants to break some curse that was put on his family for stopping humans from going extinct by making them all die after all.
Toward the end of Speed Grapher, someone with the people skills and political savvy to become Prime Minister becomes an all-consuming openly megalomaniacal beast with nothing more important to do than indulge in evil laughter and pull grotesque faces. What makes this Egregious is that before he appeared to have a plan with substantially evil implications on the lives of real people, but that all degenerates into Bond Villain Stupidity just to terrorize a little girl he claims to worship.
Rodimus in Transformers Energon. He had his own agenda and came into conflict with Optimus Prime, but mere episodes later was just one of the soldiers doing what he's told — in spite of being of equivalent experience and reputation as Optimus Prime (in the Japanese version, he's Rodimus Convoy, holding the same rank as Grand Convoy).
Also, Wing Saber in Transformers Energon. After his buddy Padlock is killed by Shockblast, Wing Saber swears he will have justice. Kind of vanishes after they capture Shockblast and he then escapes.
Also, Kicker in Transformers Energon (okay, let's just say that everybody in Energon just wanders aimlessly through the show, not really knowing what they're doing or why). In Kicker's case, his hatred of the Transformers just quietly vanishes.