Although the Puella Magi Madoka Magica franchise is about the hunt for weird-looking witches, they're actually non-malicious creatures who can't be blamed for all the suffering they have caused people. The same, however, can't be said about other species, even humans, and these villains definitely manage to cross the line.
- The fandom is divided on the Incubator Hive Mind, who takes on the form of the Weasel Mascot Kyubey when interacting with magical girls, but some of his continuity incarnations have their own Moral Event Horizon crossings:
- In episode 9, which takes place in the main timeline (known as Timeline 5 by the Puella Magi Wiki), it is revealed that he is responsible for the conflict because they need an efficient system to prolong the universe' lifespan, so he doesn't cross it by tricking the magical girls into signing the contracts that condemn them to potential witching out nor with his complicity in Charlotte's killing of Mami, H.N. Elly's mass Psychic Asssisted Suicide, or Walpurgisnacht's mass destruction of Mitakihara. However, he crosses it by the end of the episode with his lack of remorse about using needlessly malicious methods to enforce said system, particularly by tricking Kyoko into believing that Sayaka could be saved after turning into a witch, thereby leading to her Heroic Sacrifice and leaving Homura as the only magical girl to fight Walpurgisnacht - all in hopes that Madoka would contract with him.
- When the Timeline 4 Madoka becomes a witch powerful enough to destroy the Earth, the Timeline 4 Kyubey doesn't care about humanity's fate as he got enough energy from them to halt entropy.
- The suggestions from the end of the anime that Incubators and humans can somewhat coexist are completely annihilated by the end of Puella Magi Madoka Magica The Movie: Rebellion: The Timeline 6 Kyubey's actions, which are actively malicious toward the girls rather than apathetic as they were in the show and cruel even by his standards combined with his willingness to screw over the Law of Cycles (which was giving him exactly what he wanted, just not quite as efficiently) and bring back the witch system drives it home that that he is ultimately humanity's enemy, and is fully willing to destroy the peaceful relationship the instant he benefits from doing so, simply for the sake of being able to acquire more energy more efficiently.
- If his counterpart in the Magia Record universe didn't cross it by inciting a turf war amongst the magical girls during Arc 2, then he cements himself as the worst among his own versions by seizing control of the Automatic Purification System, potentially putting the magical girls in danger of witching out.
- Speaking of Rebellion, Homura crossed it for more than a couple of fans in her betrayal of Madoka and establishing herself as a devil figure, particularly the part where she erases everyone's memories. Counts in-universe, as Sayaka declares that she'll always remember Homura as a demon for it.
- Kyoko's father killing his entire family after finding out that his older daughter's wish was the only reason for his popularity, and then killing himself too. Kyoko survived but ended up bitter and amoral.
- Puella Magi Kazumi Magica:
- If Airi didn't cross it in Chapter 3 with her attack on Kazumi, she definitely does so in Chapter 4 with the revelation that she implanted Evil Nuts - fake Grief Seeds which create pseudo-witches bent on wreaking havoc - on innocent people.
- The Souju twins cross it by throwing Evil Nuts at Niko and Kazumi, which would have turned them into pseudo-witches if it wasn't for Saki's intervening.
- In Puella Magi Oriko Magica Kirika Kure may have crossed it when she released a Charlotte-like witch in the cast's school, which proceeded to eat Kazuko-sensei alive and slaughter many other innocent students.
- Puella Magi Suzune Magica: If her previous actions weren't already enough, then Kagari admitting that she made her revenge on Suzune so convoluted because it would be more fun for herself is what does it.
- Puella Magi Tart Magica
- Minou crosses it by murdering her own sister Corbeau after the latter says that she loves her sisters, even going as far to convince Lapin that only Tart and friends were involved in Corbeau's death. To make matters worse, Magia Record reveals that this was because Corbeau realized how severe Isabeau's corruption was and thus wanted the three to flee the conflict between England and France - in other words, a Heel–Face Door-Slam.
- The franchise's witches tend to have bizarre and even benevolent motivations, and are even forced to Mercy Kill humans to spare them from the Fate Worse than Death of being enslaved to the Incubators. And then there's Isabeau de Bavière, a Witch-Incubator hybrid whose purpose is to annihilate France, an entire country, and actually came into existence thanks to the greedy desire of her magical girl - a.k.a. "The Woman Who Sold Her Country" - to invade France. These facts make her the only known witch capable of crossing the MEH, and she does so by incinerating several spectators at Charles VII's coronation.
- Magia Record: Puella Magi Madoka Magica Side Story:
- Kyoko's father is not the franchise's only Abusive Parent to cross the line. Nagisa Momoe's backstory event, "Nagisa's Wish", reveals that her mother crossed it by demanding that her daughter use her one wish required to become a magical girl to murder everyone for the former's sake for no apparent reason (even if they're done nothing to her) instead of curing her illness. Given that this caused her daughter to instead make a spiteful wish and to some extent led her to witch out and kill Mami in the original series' third episode, she definitely deserved to have her organs stolen by an amnesiac serial killer in the end of the story.
- The anime version of Alina Gray crosses it when she backstabs Touka and Nemu and fuses with Embryo Eve so as to obtain Walpurgisnacht's power, with the unambiguous intent to Kill All Humans by turning them into magical girls, knowing they would be completely unaware that Grief Seeds are needed to purify their Soul Gems, effectively condemning them to witchification. And her reason for her plan: to make an art show she wants to be remembered for. Since it's already clear-cut from the franchise's mythos that witches are well-aware of their suffering, her plan and motive make her much worse than Walpurgisnacht and Kriemhild Gretchen (who want to eliminate suffering for their own twisted reasons), as does the fact that she is far more happy to throw away her humanity than any magical girl on the brink of witching out.
