It's always a rarity for an anime to end on a more somber note, and in most cases when it does, it has less to do with the villain getting a victory and more with the heroes losing one of their own. In the case of shojo series, it's more often due to a couple not ending up together as everyone would like them to.
However, there are exceptions to that. Most instances where the villain wins aren't even downers in terms of the story either, as their goals either weren't evil to begin with or they were the protagonist of the story.
10 Magical Witch Punie-Chan Centered Around A Villain Protagonist
When an anime centers around a villain protagonist, they are bound to be the one that comes out on top, and that's exactly what happens in Magical Witch Punie-Chan. She's sent to an alternate dimension to test if she's worthy of the despotic kingdom her family planned to hand off to her. By the end of the OVAs, she's more than proved herself capable of handling the crown, dispatching her sisters and anyone else who tried to defeat her in combat.
9 Rue Finds Mytho's Love In Princess Tutu
As an anime, Princess Tutu is up there for one of the oddest. The plot centers on a duck turned human trying to mend the heart of Prince Mytho, allowing him to love again. Love is the central theme here as Rue, the primary villain for much of it, continuously tries to stop Tutu from mending the shards because she fears he won't love her if he regains his emotions. By the end, Rue and Mytho manage to gain true love together, showing she had nothing to worry about.
8 Phos Is Never Able To Overcome Their Shortcomings In Land Of The Lustrous
Unlike most anime, there isn't a prototypical villain in Land of the Lustrous. Instead, it focuses on Phos' struggle to be strong, to prove they can fight alongside their other gems.
Even with augmentations, that's never the case as they are met with setback after setback, continually losing those close to them. It gets even worse when Phos realizes that the gems taken to the moon end up ground into a fine powder, making the moment when Antarcticite all the more tragic.
7 Love Is Expelled From The Afterlife In Angel Beats!
The ending to Angel Beats! is bittersweet and sad, leaving the viewer feeling bad for Otonashi. The true villain of the series isn't easy to pin down, however, the final obstacle the team has to overcome is the shadow-like programs that were created to stop love from forming in the afterlife so it couldn't become a paradise. Despite Yuri destroying them, they end up succeeding in their goal as Kanade passes on after Otonashi's declaration of love.
6 Precia's Spell Can't Be Stopped In Magical Girl Lyrical Nanoha
The collection of jewel shards is the focal point of Magical Girl Lyrical Nanoha, and for most of it, a fellow magical girl named Fate is the primary antagonist. She's trying to collect them for her mother, the true villain of the series. By the end of it, Fate and Nanoha are battling for the final time, and Precia's lack of care toward Fate is revealed as she takes the shards and attempts to dimensional jump away. Even the combined might of Fate and Nanoha aren't enough to stop her either, and Precia able to escape to whereabouts unknown.
5 Suite Pretty Cure Ends With Villains Freed From Sorrow
The villain winning doesn't always have to end up with a dour or dark ending. Suite Pretty Cure does it interestingly, allowing everyone to win. Mephisto is the villain for most of the series, trying to create a Melody of Sadness.
As the story goes on, it's revealed that many of his actions were fueled by Noise's corruption. Once free, he's able to spend time with his daughter again. The same goes for Noise, who's finally freed from the sadness of humanity and able to feel joy.
4 Ojamajo Doremi Ends Nearly Every Season With The Girl's Losing Their Magical Powers
Rarely do protagonists suffer setbacks as often as the Ojamajo Doremi trio. While they tend to save the day, it's never without some form of repercussion, often in the form of them being turned into humans again after being stripped of their witch powers. In the first season, it was to save the bad guy, Onpu Segawa. And in the second season, they are all cursed after battling the big bad of that season. Strangely, the constant setbacks work for the adorable show.
3 Quiche, Pie, & Tart Are Allowed To Return To Their World By The Mew Mews
There are times where villains become temporary allies after the arrival of an even greater threat, and that's the case with Quiche, Pie, and Tart. All three of them tried to eliminate the Tokyo Mew Mews on several occasions until Deep Blue arrives, revealing himself to be even worse. It's for that reason that the Mew Mews spare them, even giving them the final Mew Aqua to help them make their planet as beautiful as earth. It's a rare case of both sides winning.
2 Takkao Finds The Love She Desperately Wanted In Pretear
Love is often a theme in shojo, both in traditional slice-of-life shows and the more magical girl ones. Pretear is an example of how well it can be used as a plot device for a villain, making them sympathetic even as they do terrible things. Rejection turned Takkao into the Princess of Disaster. It's a feeling that persisted until the end of the series when her feelings of love are finally reciprocated by Sasame, giving her the one thing she always wanted.
1 Madoka Makes A Contract With Kyubey In Puella Magi Madoka Magica
One of the best examples of the villain coming out on top is the great Puella Magi Madoka series. As a whole, the series subverted the expectations of a magical girl series, turning them upside down. Its ending continues that trend as Kyubey got what he always wanted—Madoka made a contract with him to be a magical girl. The fact she was able to halt the creation of more magical girls doesn't change that fact at all.
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