If we're talking female antagonists, there's a %$#@load of Touhou characters. Granted, the majority aren't really evil and become Reimu's friend afterward, but there's still some truly evil ones left.
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Pictured above is Junko, one of the few unambiguously villainous Touhou characters. Originally, she was Chun Hu, the wife of the Xia Dynasty ruler Hou'yi (Who, according to Touhou lore, is now the same as the Hou'yi who shot down the Nine Sunbirds in Chinese Mythology). However, her husband killed her son and left her for the Lunarian Chang'e.
An important thing to mention is that Junko has the ability of purification; That is, to refine something and remove it of impurities. Due to the way Touhou powers work, this includes concepts. In fact, Junko used this ability on her grudge towards Hou'yi and Chang'e, becoming a spirit of pure
resentment. Apparently killing Hou'yi before the events of the game, she staged an invasion on the Moon out of spite towards Chang'e, kicking off the plot of
Legacy of Lunatic Kingdom... Which is also considered the hardest game in the series.
Yeah, it's that bad.
To pull off the invasion, she allied with
Hecatia Lapislazuli, a Goddess of Hell, the single most powerful character in the franchise, and a literal Hot Topic goth. While Hecatia isn't actually evil, she hates Chang'e as well and so she gave Junko one of her fairies. Now, fairies are the weakest beings in Touhou, but they're made of pure life force.
Since the Lunarians are pure beings with no concept of life or death, fairies are considered poison to them, especially after Junko purified the fairy into
Clownpiece... Who also becomes America Incarnate, just to tick off the Moon people more (They thought the Lunar Landing was an invasion so they don't like America).
Since the Moon is now becoming uninhabitable for the Lunarians, they then start an invasion in Gensokyo using Occult Orbs, starting up the plot of the previous game,
Urban Legend in Limbo... But that's a story for another day. Anyways, now we must stop the Lunar Capital from manifesting in Gensokyo, and so your player character of choice goes to beat up the Moon People, culminating in the defeat of the Lunarian Goddess
Sagume Kishin (Who is also a one-winged angel like Sephiroth for some reason).
Then they find out about Junko, so they go and beat up Murica Fairy and then her.
Notably, Junko's boss fight goes against the spell card rules by actually trying to kill you. Her purification gives all her attacks an element of minimalism. It's basically the Touhou equivalent of bringing a shotgun to a game of dodgeball.
And that's your Touhou lore dump for today. Went on for way longer than I expected, but Touhou's a pretty complicated series in general so I probably should've seen this coming. You're probably completely lost right now, and honestly I don't fully understand what the %$#@ is going on either.
So yeah. Junko's a pretty cool female villain. Really really unlikely but I think she fits the topic.