The relationship between master and student, or mentor and mentee, is often potrayed as a positve one. The mentor teaches the mentee everything that they need to know and protects them from danger, while the mentee feels a sense of love and gratitude. Sometimes, though, things go horribly, horribly wrong. One of the most dramatic instances of this are anime characters who slayed their master.
In some cases, this happens because the mentor turns out not to be such a benevolent person after all. That's the case with Domon Kasshu's mentor, Master Asia, both of G Gundam. Though he eventually does recant his behavior, Master Asia does try to destroy humanity, forcing his student to put a stop to him. In other cases, it's the student who betrays the master - Blackbeard was using his mentor Whitebeard to gain power, and was happy to dispose of him when the time was right. Sometimes, though, it's no one's fault. Kiritsugu Emiya of Fate didn't want to take down Natalia Kaminski, but it was either that or unleash demonic bees onto the general population.
Which of these events got to you the most?
Nagato, also known by his alias Pain, originally created the Akatsuki to promote peace within the world. But after his friend Yahiko passes away, his ideas about how to achieve that become warped. He ultimately decided that people would only pursue peace if they understood what it was like to lose everything - the way that he had, during his war-torn childhood. To that end, he stages a coup on Konoha.
Jiraiya, the man who taught him how to use ninja techniques and raised him for about three years, attempts to put a stop to his plans before they come to fruition by traveling to Amegakure. Though he's able to send information back to his comrades in Konoha, Pain takes him out in a particularly heart-wrenching battle.
Nagisa Shiota has been training to take down Koro-sensei since the beginning of the series, but when he finally gets the opportunity, it's far more emotionally devastating than he expected it to be at the start.
Koro-sensei spent several months training a group of middle schoolers in the art of assassination, but in the process he was also a great teacher, one who helped each of them become the best possible versions of themselves. He pretended that he was giving humanity a chance to defend themselves before he deliberately destroyed the planet, but the reality was that his anti-matter cells would force him to do so unless he could be stopped.
Ultimately, it's his students who stop him, with Nagisa dealing the final blow. But before he does, Koro-sensei and the kids have an emotional farewell in which they all express how much they mean to one another.
Once the captain of the 9th Division of the Gotei 13, Kaname Tousen betrayed Soul Society along with Sousuke Aizen. This was devastating news to his former lieutenant Shūhei Hisagi, who he personally mentored. Rather than being truly evil, Tousen felt betrayed by Soul Society after they refused to pursue justice for his friend who was killed.
Komamura ends up fighting against Tousen in his Hollowified form. Finally able to see after being blind in his human form, he gets to see his lieutenants's face for the first time before passing away.
Nobody in the wold of Naruto fully understands what caused Orochimaru to go rogue and start committing human rights violations left and right. Some have speculated that it might be due to his parents' passing, but there's no real consensus on the matter. Either way, he's definitely not in harmony with his former instructor and the current hokage, Hiruzen Sarutobi.
When Orochimaru attempts to destroy Konoha, Hiruzen naturally tries to stop him - and during that fight, he loses his life. In a last-ditch effort to take Orochimaru down with him, he attempts to trap both of their souls in the belly of a Shinigami using Dead Demon Consuming Seal.
Unfortunately, he's only able to seal Orochimaru's arms before Orochimaru stabs him to death.