Sephiroth. He wants to destroy the planet and other planets for absolutely no reason other than he's evil.

Kefka was insane. Insanity by no means justify crimes but it does excuse them and for someone as mentally unstable as Kefka, it is very apt.

Kuja just wanted to substantiate his own existence; to prove he was not merely a puppet or tool to be used and thrown away. What he did was wrong but he at least had a very human reason for it.

You forgot some

I went with Kefka. He killed tons of people with absolutely no remorse for absolutely no reason.

Sephiroth lost his mind after a misunderstanding. Had he not gone to Cloud's home town, FFVII would never have happened, or at least the main villian would have been Shinra. I would probably rank Rufus above Sephiroth in terms of who is more evil.

Kuja, as much as I like him, should not even be on that list. In the end he did in some way redeem himself and did change for the better at the last minute.

So Kefka wins.

Hell yes Kefka. He poisoned an entire region. Killing nearly everybody. He has no love for anyone.

Oh, he also screwed up the world entirely. One of the very few villains to actually do so.

It's between Sephiroth and Kuja for me...since I'm not very familiar with Final Fantasy VI.

Sephiroth didn't accomplish much overall, but that doesn't change the nature of his intentions. I'd go with him.

While Kefka is definitely not my favorite villain in the Final Fantasy series, I have to agree that he's probably the most "evil." Sort of like how Sephiroth isn't my favorite villain in the series, but I consider him the "coolest" (as in he probably had the most style). I say this because Kefka is basically made up of 100% pure hatred and disgust for no apparent reason. That's all there is to his character. Technically speaking, what makes him the most "evil" is that he has no real reason to be evil in the first place, at least no reason that we're told about. Kefka is insane when he first appears and insane when the party confronts him in the World of Ruin. There's no development there; he's just a vile psychopath throughout the entire game.

Other villains come across as more intimidating, such as Sephiroth and Kuja, but, depending on how you view their characters, at least one of them (Kuja) could be viewed as confused/misguided/a victim rather than genuinely evil. What separates Kefka from the likes of those two is that he's a heartless jackass without purpose. He exists for the sole purpose of being a bastard, and I must admit, he does a pretty good job. What Kefka lacks in style, he makes up for with his one-liners and evil deeds in general. That's why the average player can say that he/she honestly hated Kefka by the end of the game.

I mean, really, guys, can you honestly say that you felt any hatred towards Chaos at the end of FF1? Did you really feel like you'd accomplished something when you defeated the Cloud of Darkness in FF3? Oh, and don't even get me started on the Emperor from FF2. Yes, those villains are also evil without a reason to be evil in the first place (typically because they're just some sort of embodiment of evil or something NES-y like that), but what puts them below Kefka in terms of overall "evilness" is that...well...Kefka is a huge asshole. I mean, honestly, can anyone really feel any emotion towards a villain with no personality at all? Yeah, Kefka didn't have much of a personality, but unlike most RPG villains at the time who operated from the shadows for most of the game, he was very "in-your-face." He gave you an opportunity to hate him, which was what really separated villains like him and Sephiroth from the rest of the pack.

To recap, Kefka is a sniveling coward, the biggest asshole in the history of the known universe, a 2-Dimensional character with no depth whatsoever, and still manages to be a damn good villain because of it. I'd say he's the most evil villain in the Final Fantasy series, if only because he embodies evil without sacrificing his personality in the process. Again, he's not my favorite by any means, but I'd be a fool to say that he didn't take this title for himself.

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Sephiroth did some crazy shit as well but he was under Jenova's influence

Actually, Scrutator, Sephiroth was the one controling JENOVA. It's a common mistake, but just for future reference, the Ultimania does say that Sephiroth was the one in-control.

I voted for Kefka too. He is crazy but he had his plans on his own. He wanted to drain the powers from Warring Triad and become the god.
He accomplished that and had the whole world in his grasp. He coulda destroy the world anytime with a Light of Judgement, but he didn't. He rather had people bowing to him then have no one that bows to him.

Kefka, he acts/is a lunatic and at least Kuja and Sephiroth have a reason why they turned evil, Kefka just killed for fun and his own personal pleasure.

Even before he gained his powers he did not had any remorse whatsoever when he completely decimated the Doma Kingdom.

So Kefka is the most evil of the three in my opinion.