Bowser from the Mario series. His original motive to kidnap Princess Peach was because she was the only one who could stop his invasion of the Mushroom Kingdom. But it eventually decayed into something totally predictable: trying to get her to marry him.
Motive Decay is possibly justified in AC:Brotherhood, as the player can actually read about the motive decay of the Templars through optional documents. It's clear that the Templars' original motive of taking away free will to create stability has decayed into a flimsy excuse for oppressing the lower class as a means of protecting the interests and prosperity of a small elite. It's true that the villains of ACII were particularly fond of kicking puppies, however.
After playing AC:Revelations, it seems that this decay was largely limited to the Italian Templars. The Templars in and around Constantinople/Istanbul are a lot more well intentioned. Particularly the Big Bad.
They seem to have come full circle to being Well Intentioned Extremists again for the 3rd game however.
Also in the third game, there seems to be an implication that the same thing might be happening to the Assassins as well. At this time their motivation seems to be freedom at all costs, but one ex-Assassin snarkily points out that he remembers a time when Assassins fought for peace and that total freedom is not necessarily the same thing.
Zouken Matou's original motivation for obtaining the Holy Grail in Fate/stay night was to honor Justizia von Einzbern, who sacrified herself in order to create the Grail and was a woman he deeply admired. Furthermore, he had always dreamed of creating an utopia and to better human conditioning, even if his life and efforts weren't rewarded at all.. But over time, the deterioration of his body, senility and his frustration made him forget all of this, leaving only his obsession with immortality.
The Robot Masters in Mega Man 4 were only evil because their creator was blackmailed by Wily and they were built for practical purposes. In later appearances they are simply evil. To be fair the Mega Man series was never big on plot.
Bob and George filled a plothole lampshaded this, with the explanation being that the Soviet government took Dr. Cossack's plans and sold them to Dr. Wily, presumably because he forked over the most cash.
There remains hope. The FMV game Super Adventure Rockman goes to great lengths to remind us that the Mega Man 1 Robot Masters were perfectly good without Wily's influence, and Mega Man 9 shows heartwarming images of its Robot Masters integrating into everyday life during the credits.
Sigma from Mega Man X started off as wanting to take over the world to create a golden age of Reploids. Over the games though, he eventually seemed to just want to mess with X and Zero, even saying "I will make X AND Zero MINE!". Then in X8, he suddenly switched to a goal of creating a new world populated only by his 'children', the new gen Reploids. And then there's Maverick Hunter X, an MMX reboot series, where Sigma's initial motivation was creating a new era and pushing Reploid potential. More like Motive Roulette than just straight-up decay.
Without going into too much detail, it's been suggested that this is a result of Sigma's motives not being portrayed with adequate clarity the first time around. The underlying notion of this school of thought is that Capcom's great crime is one of laziness, rather than randomness.
When you think about it, his original motive was never really discarded. Every plan has him attempting to remove major obstacles in his path so his plans can proceed. In X1, he decided Repoids were superior to humans and belonged at the top, with himself at the very top. In X2, he tried to brainwash Zero to gain a powerful ally and destroy X, a major thorn in his side. in Xtreme and X4 he tried to destroy the Hunters through subterfuge, X3, Xtreme 2, and X7 were bids for power, X5 was a combination of several former plans,(Create large-scale chaos and destruction eliminating/distracting many who'd oppose him, gain a powerful ally in Zero, have him destroy X, proceed from there.) His motive in X8 is essentially a revaluation of his original one, that the superior beings belong at the top. Since he views himself as truly superior, only those with a direct connection him, such as Reploids with his DNA, belong in his perfect world.
Illidan from Warcraft, though always a mentally unstable guy, attacked Shattrah City for no apparent reason even though they shared a common enemy in the Burning Legion. However, previously he had been portrayed as wanting to keep a low profile in Outland. This unmotivated attack fails, resulting in his best troops deserting him and Illidan being killed in a raid.
In Illidan's initial appearance in Warcraft III, he is freed from ten thousand years of imprisonment to help his people. You might think that had driven him mad, but he does succeed in saving his people (at the cost of becoming part demon). For this heroic act, he is exiled by his own brother, Furion. Then he is hired by the demon lord Kil'jaeden to destroy the Lich King before he regains his power and an expansion for World of Warcraft. Illidan is stopped by Furion, who was misled about the former's intentions. When Furion finds out that Maiev, Illidan's jailor, had betrayed him and lied about the death of his lover, Illidan and his brother work together to save said lover. Afterward, Illidan tries one last time to stop the Lich King, but is defeated at the end of Warcraft III's expansion. Thus Illidan had been, at worst, a Well-Intentioned Extremist who rarely did anything not in his people's interest (even the original reason for his imprisonment was for keeping part of the Well of Eternity, which he felt was too useful to completely destroy, even if it is what brought the demons). Even in The War of the Ancients Trilogy Illidan, while portrayed as significantly more power-hungry, still wishes to save his people. Come World of Warcraft, however, Illidan is brooding on Outland as a Designated Villain with Informed Insanity. He is treated as if he was always a villain, carries the title "the Betrayer" (which he, in fact, mocked in the intro to the Frozen Throne, but it seems the writer's forgot that he was right), and most of the expansion revolves around fighting him and his minions, despite the fact that it is supposed to be about defeating the Burning Legion's Burning Crusade, whom he betrayed and is now using their weapons against them. To put salt in the wound, Maiev helps you defeat him, who was not only said to have died in multiple sources, but was the true traitor in Illidan's story, having left the night elven leader's lover for dead and allowing the Lich King to survive just for a chance to imprison somebody who was saving the world.
The Betrayer title was given to him back during the war of the ancients, not after WC 3. Due to him first betraying the good guys to join the legion, then double crossing them when he realized they were too evil, then (in his people's eyes) Betraying them again by recreating the very thing that had started the war to begin with simply to feed his own addiction. Illidan really does have a hard time staying on one side for any length of time.
Maiev herself suffered from this. Her original goal was just to be a jailor and deal out justice. After 10,000 years locked in a jail guarding prisoners, her motive warped to one of simple vengeance. By the end she has become vengeance incarnate itself and only cares about dealing with Illidan. When she helps you kill him, she mocks him the entire time. It's clear that she is having fun fighting him. When Illidan is killed, all she is left left with is emptiness. She finally realized that her goal was the only thing that kept her going for the majority of her 10,000 year life (which, by the way, is going to end soon due to the World Tree dying). She leaves the battle completely broken.
Kael'thas in Warcraft 3 was a sympathetic character who allied with Illidan because he had no other choice and wanted to save his people. In World of Warcraft, he has become a power crazed evil overlord and demon worshipper who would gladly kill off his people to ensure the victory of the demons. One of whom is the very demon that arranged for his people's decimation in the first place.
Arthas has largely the same storyline — he starts out making difficult and heartbreaking decisions (the big one being killing off the entirely innocent population of Stratholme to prevent them from becoming undead minions of a big bad) and devolves into becoming a simple insane Big Bad himself. He only averts this trope because his fall into insanity was planned from the beginning, rather than something that was tacked on.
Following the trend, the Big Bad of the fourth expansion, Garrosh Hellscream, suffered noticeable decay after he was convinced to actually act like a leader. Originally trying to uphold the traditional values of the Orcs, his actions to defend them became increasingly extreme and his Blood Knight tendencies more pronounced. His abrupt decision to nuke Theramore, despite having previously executed a general for a similar act, and his increasingly crude methods of running the Horde after that marked the end of his "to protect my people" motives and the beginning of his "I will conquer the world by any means and erect mountains of skulls" motivation.
Aribeth in Neverwinter Nights went from defending the city, to taking vengeance on the people who didn't actually kill Fenthick but she blamed for it, to having a vague plan to enter their citadel, to joining them and destroying the city she now blamed for the earlier spoilered event.
Though having a ten thousand year old lizard-person Mind Rape her every night kind of drove her a bit insane
Forcing a paladin to Tyr, God of Justice, to live with the fact that she's serving a city that demanded her lover be put to death out of a misplaced desire for "justice" over the plague debacle actually makes for a very good treatise on what should actually make a paladin fall.
While technically neutral, there's been major debate among fans on whether or not Scorpion from Mortal Kombat has fallen to this trope, all hinging on whether or not his ending in MK II came to pass; up until then, he had come back to slay Sub-Zero to avenge the death of himself and his family and clan, but according to the ending, he notices Subby spare an opponent, and deduces that it's not the same man (in fact, the guy's the original Subby's younger brother). If true, from then until MK 4, Scorpion swears to protect the new Subby as atonement, giving him a modicum of depth that proves he's not the revenge-crazed one-track-mind spectre he would be if the ending never happened. This is all rendered moot when Deception gave him a higher calling than simple vengeance, but even that was screwed up, and now he's on another revenge kick.
Zemus of Final Fantasy IV starts out a Lunarian Supremacist. By the time of the game proper, he's more into Kill All Humans. When his body is destroyed, his soul quickly becomes the personification of hatred.
Sephiroth in Final Fantasy VII initially turns evil after going mad from the (partly false) revelation about his origins and deciding to take revenge on humanity on behalf of his mother whom he believes to be a Cetra. After he falls into the Lifestream and floats there for a few years, he returns having decided that it's actually all right that his "mother" is an Eldritch Abomination (the one who nearly wiped out the Cetra), and decides to absorb The Lifestream to become a god and acquire ultimate power. Then Cloud defeated him for a second time. In almost every spin-off since Sephiroth is little more than Cloud's archrival, obsessed with defeating him but not before MindScrewing him by pointing out how easily he can push Cloud's buttons. He did have a new plot to take over the world in Advent Children, but he set it aside in the climax for a duel with Cloud and his plan failed when Cloud beat him. The accompanying novellas reveal he didn't even have to recreate a physical body for himself to see his plan succeed, he chose to do it just to rub his rebirth in Cloud's face. At this point Sephiroth is little more than the personification of Evil Is Cool, striking iconic poses and dropping quotable one-liners about despair before going off to duel Cloud again. The novellas justify his obsession with Cloud by explaining that his hatred was the only thing that allowed Sephiroth to maintain his individuality in the Lifestream. Sephiroth kept his ego from being absorbed by the Lifestream by thinking really hard about how much he wanted to beat the crap out of Cloud.
Dissidia: Final Fantasy has a subtle Lampshade Hanging of this—when Sephiroth senses Cloud approaching, he tells Warrior of Light he must "fulfill his obligation" and goes off to see Cloud. When they meet Sephiroth squares off to fight, but Cloud refuses because he doesn't see the point of fighting him anymore. No, really, he says "Fighting you would be meaningless. I'm tired of taking part in pointless battles." By the end of the game, his fixation on Cloud has grown obsessive.
This is lampshaded in Fallout 3. In the Hubris Comics building (a parody of Marvel/DC), you can find a letter to the editor from an irate fan complaining about how the new writer of Grognak the Barbarian has reduced the villainess "the AntAgonizer" from a complex, sympathetic antagonist to a 2-dimension cardboard villain. Later in the game, you can even use the argument to persuade a woman who has based her entire persona on the fiction Antagonizer character to give up her life of supervillainy.
This happens in-universe to the west-most sects of the Brotherhood of Steel by the time Fallout: New Vegas rolls around; their motive of redeeming the wasteland has decayed into basically being thugs with power armor that "confiscate" any high-tech pre-war goodies that people outside the Brotherhood find. A maverick scribe Veronica has her companion quest center around her futile effort to avert this.
In Devil May Cry, Lady continued on her path as a Devil Hunter at the end of the third game (rather than go back to a regular life) because she had "a job to do that's far from done, which is to eliminate every last demon", to ensure that monsters like her father never came about again. Seems heroic, right? Too bad you won't be able to tell. The animated series has her saying that she stays with the job, not out of a sense of heroics or a greater goal, but because she has an insatiable need to kill things. That's that.
Trent Hawkins, the hero of Tyrian lampshades this happening to him. Originally starting out to get revenge on the Mega Corp. that killed a close friend, he ends up getting pushed into to ever more dangerous missions often only tangentially related to anything he actually cares about. Eventually, by the end, when he realizes that he "doesn't even remember the name of his friend killed in episode one", he just decides to Screw This, I'm Outta Here!.
Ganondorf was revealed in The Legend of Zelda: The Wind Waker to have begun his conquest/invasions intending to make a better life for his people by getting them a home that wasn't as harsh and uninhabitable as the Gerudo Desert. Unfortunately, as The Legend of Zelda: Skyward Sword implies, he's been latched onto as the host and implement of an ancient demon's death-curse, resulting in a rapid decay of his motives from "a home for my people" down to "Omnicidal Maniac" in a matter of months whenever he tries - judging from what we see, the decay took place entirely during or before his first appearance in The Legend of Zelda: Ocarina of Time, its just that Link (and thus the player) don't get to learn what he started out wanting until Wind Waker.
Walker (and by extension, the player) experiences this throughout Spec Ops: The Line. As the situation in Dubai worsens, the Deltas lose sight of their desire to evacuate the city, which is exacerbated when Walker beginns to hallucinate and direct the team's attention to destroying the 33rd. Later in the game, everything, from the words of a hallucinated John Konrad to the loading screen itself, is used to call Walker (and the player) out on this.
"Do you even remember why you are here?"
The Didact of Halo started out as a Reasonable Authority Figure who did not want to fire the Halo superweapons because he knew they would destroy billions of innocents along with the Flood. With a change of writers came a change of motive, and the Didact of Halo 4 has become more of an imperialist, who would go as far as to attempt genocide on humanity (twice!) to turn their bodies into droid soldiers solely to avoid firing the rings. Halo: Silentium works to justify his descent, revealing that not only did the Flood drive him mad, but when he was then sealed in can/Cryptum for a hundred millennia, he was awake the entire time. It also retconned the previous reasonable actions of his to have been done by a clone of him, so that the original was always a bigot.
Max Payne is an unusual example of the protagonist experiencing this. In Act 1 he's mainly interested in tracking down the supplier of Valkyr and finding out who murdered his partner, but his Cowboy Cop tendencies get noticeably further out of control as the game progresses... And then he does track down the supplier of Valkyr and learns several important facts about them (starting with the fact that they murdered his wife and baby daughter as part of a cover-up) and... Well, he's not really interestedin collecting evidence anymore.
Supplementary materials for the third game reveal that the Crachá Preto paramilitary Hired Guns started out as law enforcement types going Vigilante Man in order to eliminate the crooks that the law couldn't or wouldn't touch. Then they lost their way.