A mentor once had a student, who used to be a good person, and perhaps the mentor's most promising and skilled student ever. But that student had a flaw, a seed of villainy that just needed a trigger. Usually, it was arrogance about his/her skills, or impatience at not being taught the final skills that the mentor had yet to teach. Then the student became a villain, even the Big Bad.
Sometimes the mentor is the protagonist, and will have to take the student down in the story. But far more often the protagonist is another student the mentor takes on. If that's the case then the other student is the Mentors New Hope.
Compare Deceptive Disciple (when the student was evil the whole time, just pretending not to be), Fallen Hero, Merlin And Nimue, and The Paragon Always Rebels.
Do not put examples unless it was clearly stated the pupil was good beforehand. If it turns out the pupil wasn't, that's Deceptive Disciple.
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Anime and Manga
In Alice 19th, Darva was originally Master Lotsuan's disciple.
In Soul Eater, Asura was Shinigami's apprentice until he went insane and threatened to destroy the world, and had to be sealed away.
Naruto offers both Orochimaru and Sasuke. Orochimaru was considered the village's best ninja when he was in Konoha, then got fed up with things and left for his various evil deeds. Sasuke was lured away by Orochimaru.
There's also Nagato, also known as Pain, a former apprentice of Jiraiya. More of a Well-Intentioned Extremist, but he still qualifies because he puts such a heavy emphasis on the "extremist" part. Especially since his 'good intention' is to invent a chakra nuke and use it so that everyone will be too afraid to go to war for a few generations.
The Third Hokage notes that he always suspected something was amiss about Orochimaru, so it's unclear when exactly he turned evil, even if he was evil before he left the village (around the time the Third Hokage chose Minato for the position of Fourth Hokage largely because Orochimaru was untrustworthy.)
Apparently a younger Orochimaru was 'good' enough to cry when Dan died. Wherever he started, he did a lot of falling.
He was also always Hiruzen's favorite, just to drive in the Sasuke parallel, so the old Professor can't have suspected too much.
He suspected, but he thought that since it was a time of war a kid with malice and ambition might end up being useful, so long as he could be guided and controlled. He later admitted he let his pride blind him. Oro only left the Leaf after commiting a series of brutal murders and human experiments, and being caught, so he was definitely bad before he outright defected.
Then there's Obito, who became Tobi, the leader of Akatsuki and The Dragon to Madara Uchiha. Like Orochimaru and Nagato, he played a big role in the death of his former teacher. However, unlike most examples of this trope, his teacher never even knew that he had turned evil, or that he was even alive.
Full Metal Alchemist pulls a variation, in that Homunculus kind of mentored Slave #23 from the day he gave him his name...but recognized Van Hohenheim as 'his father.' Given his entire identity is later molded around the fatherly role, this concept is clearly significant to him.
In episode 10 of Samurai Champloo, the gang meets up with a friendly monk who turns out to have been a former martial arts teacher who once taught Shoryuu, the villain of the episode. He had encouraged Shoryuu to travel and hone his skills, but this went horribly wrong, when after learning an amazing technique, Shoryuu became obsessed with proving his greatness by challenging and killing any martial artist he could find.
Betelgeuse in the movie Beetlejuice, worked for afterlife case worker Juno before he became a "freelance bio-exorcist."
Clu from TRON: Legacy. He took Flynn's original programming for him too far, and warped it. The comic Betrayal, however, indicates that he probably wasn't all that good to begin with, and Flynn was just too distracted by the pressures of his life in the analog world to notice until it was much too late.
Somewhat undercut when the audience learns that De Nomolous was Rufus's old gym teacher.
In X-Men: First Class, the mutants all train together as part a CIA team to fight Sebastian Shaw, but Angel Salvadore decides to join with Shaw, shortly after she is recruited by the program. At the end of the film Erik (Magneto) and Raven (Mystique), after defeating Shaw become the new Big Bads and turn against Charles Xavier, whose ideas about Mutant-Human relations differ from the ones they have, to form the Brotherhood.
The Vietnamese gangster in Big Stan was The Master's star pupil.
Sauron, the principle antagonist of Tolkien's The Lord of the Rings trilogy, was a Maia in the First Age under the tutelage of the Vala Aulė the Smith, and went by the name Mairon, before Melkor the Morgoth corrupted him to his cause and made him his lieutenant. When Morgoth was defeated, Sauron essentially became self-employed and sought to dominate Middle-Earth himself.
A startling number of Luke Skywalker's Jedi students, in the Star Wars Expanded Universe, end up eventually falling to the Dark Side. He's able to bring some of them back. Brakiss intended to be a Deceptive Disciple, but Luke believed he could be turned; Brakiss started Becoming the Mask until Luke put him through a test which horrified him and caused him to flee. Luke always believed that Brakiss could be redeemed, and in The New Rebellion parts written from Brakiss's point of view suggest that he'd like that, but it's not to be.
Played word-for-word straight by Jarrod in Power Rangers Jungle Fury. Rio, his counterpart in Juken Sentai Gekiranger, follows roughly the same path, but there is no single trigger that causes him to switch: he simply becomes dissatisfied with the progress he's making under the good guys.
Gekiranger also had the three Kenma, precursor villains who turned on the founder of Beast Fist after their leader learned he was the *second* choice for successor. This led to the Kensei sealing them away until Rio and Mele let them out.
Forgotten Realms setting. Elminster isn't really into it, but he taught a lot of wizards in his years, and the main requirement was the talent, not moral qualities — it's Mystra's priorities and not that her own avatars never were downright villainous. So... Sammaster — though after being "certified" by Mystra and before fully going nuts. The Shadowsil — became an evil archmage, worked in late Sammaster's little club, virgin sacrifices and all that. Raerlin — the guy has a dubious achievement of saying "Death has come for you at last, Old Mage" twice: once while alive, once as a lich. And so on, and on.
Horus in Warhammer 40000 used to be the most trusted Primarch of the God Emperor, who treated him like a son. Then Horus gets corrupted by Chaos and leads a rebellion that results in trillions dead, the Emperor in a coma, and the future of the Imperium in peril.
According to the manual for the original Banjo-Kazooie, Gruntilda the witch was a student of Mumbo-Jumbo's until she turned evil... and to pay him back, she turned his head into a skull-shaped metal mask. It seems to have been Ret Conned, though, with Grunty's Revenge (which takes place in the past) has Mumbo Jumbo as an up-and-coming shaman without a pupil... and a face that's still skull-shaped.
In the backstory of the firstFire Emblemgame, Gharnef was once a pupil of Gotoh, the White Sage. However, when Gotoh passed the legendary magic tome Aura on to his other pupil Miloah because Gharnef, while a good man, lacked compassion, he was overcome by jealousy and stole the Darksphere, a cursed artifact that twisted him into the cruel Evil Sorcerer seen in the game proper.
Demolitions expert Peter Stillman confesses to giving rise to Metal Gear Solid 2's Mad Bomber, Fatman. Stillman poured all of his knowledge into his surrogate son, unaware that Fatman was an obsessive fame-seeker whose infamy would put the Unabomber to shame.
"I didn't teach him the most important thing I had to tell him. There are some things you have to pass on. The trick is to know which one. Right... All I taught him were skills. And now I have to stop him from using it to destroy us all."
In Tekken, Feng Wei, whose design is actually based on evil kung fu villains of the 70's wuxia flicks.
Uther Lightbringer and Arthas Menethil in Warcraft III were much like Obi-Wan and Anakin.
Fukushima from the Kim Possible episode "Exchange" was a student of the Yamanuchi Ninja School. He turned out to betray the school and helped Monkey Fist obtain a powerful weapon. It's not really explored why he did so, either he was already paid by Monkey Fist, or he only turned after Ron came to Japan. He could have felt insulted that Ron received honors that according to him should not be given to "outsiders". Or else he became jealous of Yori's shows of affection for Ron.
In Dungeons And Dragons, the Dungeon Master revealed that Venger was a former pupil. In the unaired series finale Venger is revealed to be Dungeon Master's son.
Transformers Animated. While never really elaborated on, Lockdown was once a pupil of Yoketron's. At some point, he abandoned the Cyber-Ninja dojo - only to return, sometime after Prowl joined, to make off with the dojo's protoforms and to kill Yoketron. Oilslick may also apply for this trope, but with the lack on information on his past, it's debatable.