I already noted that the women are in the minority when it comes to the main heroes, but when it comes to the "evil" side of the story (although the antagonist is not necessarily evil), there the women also form the minority.

In this list I'll mention some female antagonists

Please note, that some antagonists are only revealed halfway the game or sometimes even at the end so a spoiler alert is in order!

Tyr - Breath of Fire

Now I must note that in Breath of Fire I many names have been changed in the English translation, as in the Japanese version her name is "Myria", just like the BOF3 antagonist I also included in this list.

Her role as main antagonist is a bit debatable as the story first circles around Zog and later about Jade, both dark dragons, however as the dark dragons fight for the favor of Tyr, the Goddess of Desire, which has been mentioned in the start-up story you see even before you leave the first town to start your adventure, I think it's safe to call her the game's main antagonist.

Now Tyr's own agenda is unclear. This has to do with the story in Breath of Fire I being a bit minimal (especially when compared to the later installments), and also due to the very poor translation of the game. For what is clear she shows herself as a kind woman fulfilling wishes, while she is in fact an evil entity. If Ryu has obtained the "Agni" dragon form, you can force her into her true form, which is that of a horrible monster.

Nice to note is that the mural shown in both the title screen of Breath of Fire III, and in the corridor leading to the hall of Dragon Elder Jono, depict the battle against her, although there is no clear relation between Tyr and Myriah, due to the story lines following a completely different kind of course.

Myriah - Breath of Fire III

Myriah is the main antagonist in Breath of Fire III, although her existence is not mentioned until the end of the first part. The "childhood part" as we often call it. Even though her image is shown at the star the start of the game (like in the shot above). Myriah is the mother goddess of the world and protector of all life living on it. She saw the dragons to a threat to all other life, and decided to exterminate the dragons. You are the last dragon, and as such the goddess her fixed her eyes on you. Even though she's your enemy she does care about you, but when you refuse to give up your powers as a dragon, she sees no other option than to kill you.

Mother - Wild Arms

Mother is the ultimate destroyer of everything in existence, only seeing the beauty in things that have come to an end. When she tried to attack Filgaia, the world on which the game takes place, the people of Artica somehow lured her into a trap and could imprison her in a cocoon. The Quarter Knights free her in order to get their queen back, however they didn't know that it was also the same Mother who destroyed their home world Hyades. The Quarter Knights set up a plot and use the heroes to destroy her, having clean hands themselves, however, it will appear that Mother didn't die, and eventually she manages to devour Zeikfried, the leader of the Quarter Knights and to assume his shape. The heroes will eventually face her again in the shape of Motherfried.

Beatrice - Wild Arms 3

Beatrice is the main antagonist of Wild Arms 3, although this is not revealed until the game's very last chapter, although many hints to her are in the game, and you can even see her loads of times in random places, but not reach her. Just before the boss Humbaba you can even hear her laugh in the distance (the heroes even take note of that).

Don't let the fact that she assumes the shape of a cute little girl fool you. She is dangerous.

Beatrice is a dream demon. She is only able to exist inside the digital library Hyades, although she can manifest herself also in people's dream, hence the name "dream demon". Beatrice resents her own existence as a dream demon, bound to a digital library, and wants her own world. Her first attempt was when she entered the dreams of the scientist Duran, a member of the Council of Seven, in the Yggdrassil project. This caused the project to go wrong, killing all seven members of the council (including Werner, the father of main protagonist Virginia Maxwell) laying the world of Filgaia (where the story takes place) in waste, so far that even the seas and oceans dried up. The outcome was not fully what she desired. Things went worse on her when three members of the council where kind of resurrected by Hyades and came back as the Prophets who wanted to terraform Filgaia for their own survival. (A 4th members was also resurrected this way, but chose to fight against them). Beatrice decides to enter the dreams of the young boy Shane (younger brother to playable character Gallows) and through him the heroes get involved in the story, and technically she uses the party to get rid of the Prophets, and the demon Siegfried they summon. When that is done she tries to sacrifice Shane in order to use his pillar powers to obtain her goal, but this goes wrong when Gallows stops Shane, and that is the moment she properly introduces herself to the group. She will still insist on creating her own world, her own Filgaia and is willing to sacrifice the existing Filgaia and all life living on it to obtain it. Not to mention to devour people's memories in order to shape things well.

Jenova - Final Fantasy VII

Now I see the angry reactions coming as Sephiroth is supposed to be the game's main antagonist, but the truth is that Jenova is. It was Jenova who killed president Shinra. It was Jenova who killed Aerith. It was Jenova who tried to destroy the world with the Black Materia. Actually it was Jenova who was behind almost everything.

Jenova is a kind of alien who destroys all that comes in her path. Many worlds and civilizations have met their end thanks to her. When she came to the world where the story takes place, it was her to annihilated the Cetra (of which Aerith is the last survivor), however Jenova fell in the hands of Shinra wear mad scientist Hojo did the craziest things with her body which was by far more potent than a human body. Hojo created Sephiroth by mixing his own DNA with that of the woman Lucretia and also of Jenova.

Now the story is very unclear on many points, partially due to mistranslations, and I really hope the new version of the game may shine more clarity on matters. We know that Jenova eventually become too much for Shinra to control and broke free. She assumed Sephiroth's shape and did many horrible things along the way. When you meet Sephiroth on the boat to Costa Del Sol, he doesn't recognize Cloud, even though Cloud was there when Sephiroth destroyed Niebelheim (he really was, but some revelations later will work confusing). This was not Sephiroth but actually Jenova. Cloud has some cells of Jenova injected and that caused him to almost kill Aerith in the ancient city of the ancient as Jenova tried to control his body. As she failed to make Cloud do it, as he could resist her, she came down disguised as Sephiroth and killed Aerith herself. The first time in the game, the real Sephiroth is shown might actually be in the area were Cloud hangs upsidedown next to Sephiroth, handing over the black materia, which is past the half of the game. The threat posed to the world due to Jenova and Sephiroth having the power to summon Meteor and destroy the world as a result is what awakens the Weapon monsters.

What is clear to me, as a lot of the story is still unclear, is that even though Sephiroth gets the credit, it is actually Jenova who truly runs the show.

Yunalesca - Final Fantasy X

I know this entry is quite controversial, as FFX does not really have a clear antagonist, but if you know the story and its backgrounds well, you can safely come to the conclusion that she is the mastermind behind all of Spira's suffering, or at least, the most important part of it.

Yunalesca is an unsent, meaning she's actually dead, but that her attachment to the world of Spira (on which the story takes place) caused her to keep existing and living on. Yunalesca was born in Zanarkand as the daughter of summoner Yevon, and she was married to Lord Zaon, this much is already told by Seymour halfway the game. Seymour does not tell the WHOLE story, though.

The misery began when there was a war between Zanarkand and Bevelle. Bevelle had loads of powerful machina weapons and the summoners of Zanarkand didn't stand a chance. Zanarkand was doomed. Yevon took the souls of surviving people in Zanarkand and turned them into Fayth, statues from which Aeons can be summoned, some kind of spiritual entities (you find these fayths halfway Mt. Gagazet), and Yevon created a new Zanakard with it, known as "Dream-Zanarkand", and there Zanarkand would keep on existing, forever, untouched by its enemies. In order to keep himself, and thus Dream-Zanarkand safe he created Sin.

Yunalesca knew that Bevelle's machina were strong enough to destroy Sin, and her father who resided within Sin, and that Zanarkand was therefore even as a dream, not safe. And she founded the Yevon religion (and this also answers the question why the teachings of Yevon ban the use of machina). She did not find many believers, and particularly in Bevelle she was not successful. So she came up with a very good ruse, that would dominate Spira for a thousand years. She made up the stupid story that a summoner can defeat Sin by means of the "Final Aeon", already aware that Yevon would merge with the Final Aeon and turn it into a new Sin. She "backed it up" by sacrificing her husband Zaon, and showing the world how it was done. Just like the summoners after her she died in this process and became an unsent, so she could help the summoners after her to do the same. When Sin came back after Yunalesca's calm, some people already followed her teachings, others did not. When Gandof was the the first one to follow in Yunalesca's footsteps and to defeat Sin, people considered the teachings of Yevon as "confirmed" and the Yevon religion took over the world. While people believed that Yunalesca founded the Yevon religion in order to give the people hope, the truth is that Yunalesca's prime goal was to keep Sin living forever and to keep the people dumb and ignorant. Since she is the mastermind of why Sin keeps coming back and why the world is bullied by the Yevon priesthood, I deem her (and not Yevon and Sin) the main antagonist of Final Fantasy X. Even though defeating her is not the game's main objective. I know this is kinda debatable, but I have thought this trough.

The Goddess - Star Story

I will not tell you too much about her 😜
The Goddess is the main antagonist and final boss of Star Story, and the reason behind the Astrilopups (an alien race) hunting down the game's main protagonist Wendicka Lovejoy.