More often than not, anime villains are either defeated or killed by either irony or karma. This manifests literally in a number of ways, with the most common being their own mighty powers used against them.
Sometimes, the anime's hero figured out a way to use the villain's own abilities against them, or the villains did it to themselves in a case of ego and hubris gone awry. Whichever scenario is followed, it's hard not to deny that these bad guys had it coming.
WARNING: Spoilers ahead.
10 A Certain Scientific Railgun — Therestina Kihara Lifeline's Artificial Railgun Lost To The Real One
As a Level 0 esper (or a person with no powers), Therestina still suffered from a severe inferiority complex despite her heightened genius-level intellect. This drove her not just to join other fatalistic scientists' quest to achieve the theoretically impossible Level 6 but to also make her own powers through engineering and science.
Therestina rode the heavily armed HsPS-15 power armor, which came equipped with its very own Level 5 railgun that was a mechanical copy of Mikoto Misaka's Electromaster abilities. In their final showdown, Therestina's powerful railgun was outmatched by Mikoto's railgun and determination, both of which surpassed her cold calculations.
9 Tokyo Ghoul — Kureo Mado Was Killed By A Ghoul's Kagune After Desecrating Them
Normal humans would barely survive in a fight against a Ghoul, so the solution was the creation of special weapons known as Quinque. These armaments, however, were made from the harvested Kagunes of dead Ghouls, which the Commission of Counter Ghoul then reverse-engineered into weapons for their agents to wield.
The sadistic CCG agent Kureo Mado had two powerful Quinques, both of which were ripped from the bodies of Hinami Fueguchi's parents. Determined to kill the Ghoul child, Kureo hunted her down and was killed for his troubles. Before dying, his beloved Quinques refused to attack their daughter, giving Touka the opening to land the killing blows with her own Kagune.
8 Baccano! — Dallas Genoard's Immortality Condemned Him To Drown Forever
Dallas and his buddies were nothing more than low-level hoodlums, but they got a lucky break when they bumped into Szilard Quates. The immortal villain needed some goons, so he gave Dallas and his gang an incomplete version of the original immortality elixir which granted eternal life but not ageless eternal youth.
Szilard never told them about the elixir's limits, though, so Dallas' gang ran around killing the Gandor Family's people in a bid to enact a hostile takeover. This backfired when the Gandors (who were also immortal) captured Dallas's group, cemented them in barrels, and threw them in the Hudson River, where they'd repeatedly drown to death for eternity.
7 Naruto — Orochimaru's Absorption Technique Backfired Horribly
The key to Orochimaru's apparent immortality was the Living Corpse Technique, which allowed him to transfer his consciousness between bodies by taking over the host's mind. After training Sasuke Uchiha for some time, Orochimaru planned to use his new student as his latest vessel. That said, he never expected Sasuke to turn things around.
Orochimaru successfully got into Sasuke's mind and was in the process of taking over, until Sasuke activated a sealing spell. Not only was Orochimaru overpowered, but Sasuke trapped him in a prison in his mind, where he languished for a long time. In brief, Orochimaru's ideal new host body instead became his hellish prison.
6 Fullmetal Alchemist (2003) — Shou Tucker Turned Himself Into A Chimera Through Alchemy
There are some key differences between Fullmetal Alchemist and its reboot, Brotherhood. One example is Shou's fate after merging his daughter Nina with his pet dog into a Chimera for science's sake. While he was summarily executed in Brotherhood, he was forced to live with his sins in the 2003 anime.
Now working for Laboratory 5, Shou desperately tried to resurrect Nina through alchemy, but this only resulted in lifeless husks. One incantation, though, rebounded and turned him into a monstrous Chimera. Worse, the combined stress of his guilt and predicament ate away at his sanity, which culminated in him losing his mind by the series' end.
5 Bleach — Baraggan Luisenbarn Wasn't Immune To His Own Aging Powers
As the Espada who embodied death by age, the old and vengeful Barragan had the ability to age anything into ash by using his Respira. The Respira also served as an impenetrable shield that deteriorated any attack fired at him, rendering Barragan almost impervious. Little did Hueco Mundo's former god king realize that his powers would be his downfall.
After his arm was caught in the Respira, Hachi amputated it and teleported his rotting limb into Baraggan's body. The Visored theorized that if Baraggan's power was as absolute as he boasted, then even he wouldn't be immune to its wrath. Hachi's hypothesis proved correct, and Baraggan decayed into nothing from the inside out.
4 JoJo's Bizarre Adventure — DIO Found Himself At A Time-Stopping Stand's Mercy
When he returned from the bottom of the ocean floor, Dio Brando was reborn as DIO: a nigh-immortal vampire who was also a Stand user who had the powerful The World at his beck and call. The World could stop time for a few crucial seconds, which DIO would then use to torturously toy with his prey for his own sick pleasure.
However, DIO found himself at the receiving end in Stardust Crusaders' epic final fight. With no warning whatsoever, Jotaro Kujo's own Stand (Star Platinum) learned how to stop time. Before Jotaro punched him so hard that he exploded, DIO learned what it was like to be helpless yet completely aware while under another Stand's influence.
3 My Hero Academia — All For One Was Defeated By The Quirk He Gave To His Brother
Long before My Hero Academia began, All For One was already a powerful supervillain who could give Quirks to his disciples or take them for himself. In a bid to get his Quirkless younger brother Yoichi Shigaraki to join him, All For One gave him a new ability. This, however, was the birth of the one Quirk that could defeat All For One.
Yoichi actually had a Quirk, but it was the subtle ability to pass power to others. All For One, meanwhile, gave him a Quirk that stockpiled powers. Together, these formed One For All: the stacking generational Quirk that All Might used to decisively defeat One For All. That being said, One For All anticipated this and planned for his own defeat.
2 Puella Magi Madoka Magica — Kyubey Doomed Themselves By Unlocking Madoka Kaname's Godhood
From the beginning, Kyubey and their fellow Incubators wanted to unleash Madoka's untapped godlike powers. The only way to do so was to trick her into becoming a magical girl who'd either die fighting a witch or become one, the all-powerful Kriemhild Gretchen. In this deconstructive magical girl anime's climax, Rebellion, the Incubators got what they wanted, but they regretted it shortly after.
By experimenting on Homura Akemi, Kyubey hoped to awaken an amnesiac Madoka's godhood and control her to rewrite the Law of Cycles in their favor. Madoka recovered her memories, but then Homura stole her power and remade the Law of Cycles in such a way that the Incubators, instead of magical girls, bore reality's suffering.
1 Neon Genesis Evangelion — Gendo Ikari Was Killed By The Metaphysical Apocalypse He Initiated
Despite directing NERV's fight against the Angels, Gendo had no interest in protecting mankind. In truth, he wanted to end the world by harnessing the powers that created the Angels in the first place. By The End Of Evangelion, Gendo had the fate of the world in his right hand as he fused with Adam's embryo to become Human Instrumentality's trigger.
Gendo's last step was to merge with Rei, who harbored the soul of Lilith, and become a god who could recreate the world. However, Rei betrayed Gendo and gave the power to Shinji, the son he abandoned and abused. As humanity was welcomed into one consciousness by visions of their loved ones, Gendo died alone at the hands of an enraged Eva Unit-o1.