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For me Its the prophets. They just scoot around in there chairs touching Unngoys, abusing power when they physically cant lift a paper weight. Yet somehow they convince even the most powerful such as brutes to fight along there side. If not any of these post honorable mention that I missed.
Prophets when I think halo bad guys I immediately think covenant. And the covenant are led by the prophets.
In my experience as a writer, I have discovered that a good villain is made when you are able to sympathize with them. The Prophets and Ripa Moramee were just radical, Tartarus was a sociopath swayed by lies, and the Gravemind was just pure, unadulterated evil. Don’t get me wrong, all of these characters were top notch villains, but here are my top three:

3. Atriox
At first, you are made to think that Atriox is just an angry Jiralhanae that has a passion for blood sport, but his backstory reveals something more tragic. He hates the Covenant for what they did to his pack. They sent them to die over and over and over again. One day, as anyone would, he snapped, and the best part is, you can understand why. I would have him higher on the list, but unfortunately we haven’t had much time with him. Hopefully he’s developed in more in future games.

2. Guilty Spark
Guilty Spark is a poor sap who is just trying to follow orders. Activate the rings, contain the Flood. Unfortunately, this big green dude keeps getting in his way, and destroying the thing he’s supposed to protect and curate. Oh, he killed Johnson? Wouldn’t you? The man is about eliminate your sole purpose in life. Sometimes drastic measures need to be taken.

1. Didact
“The Mantle of Responsibility for the galaxy shelters all, human. But only the Forerunners are its masters.”
-Ur-Didact.
The Didact began as a simple Forerunner Warrior-Servant, doing his best to assure his people’s place in the universe. I mean, of course the were the Reclaimers of the Mantle. They were the most advanced beings in the galaxy. The Flood are a threat, yes, but the shield worlds will ensure his people’s safety. Now the Builders are proposing what? To create an array of weapons to eliminate all life in the galaxy? What good will that do? That will only lead to the fall of the Forerunners! He built the shield worlds anyway, knowing his plan was the most effective survival tactic.
Now, put yourself in his shoes, your people think you’ve gone mad. Your own wife has betrayed you. You are just doing what is right for your people, but instead your are being imprisoned.
When the Didact was released, he learned that his people were all but extinct, and these humans were now taking up the Mantle. This revelation, combined with his millennia of silent rage filled contemplation, has now thrown him over the edge. He calls up his only allies, the Prometheans who once served him, and a practically useless bunch of species who consider him a god, and use them to assure you, the last Forerunner, your rightful place.
Yet, you are still defeated. Defeated by an Ancilla, a human, and an impression of your lost love, tasked with stopping everything you’ve worked for.
This is injustice.

The Didact hits number one for me, because in his mind, he is trying to do the right thing, and everyone he is sacrificing for is against him. You can hear in his voice and occasionally see on his face the pain he experiences, and the books make that even more apparent.
The Prophet of Truth. He had it all planned out. Him and the Emperor from Star Wars would’ve been best buds. 😄😁
Prophets for sure but I love Gravemind in H2A.
Going with the Gravemind. He's been the bad guy since the start really. The Primordial was the first Gravemind in every way that matters, and every Gravemind since has had the knowledge and power of all the Graveminds that came before it.
the prophets
Prophets if rated together. The single best villain in Halo history has got to be Tartarus.
Gravemind is the best Halo villain. The Flood is responsible for everything: The creation of the Halo Array, the fall of the Forerunners, they even used to be godlike creatures. EVERYTHING. The Gravemind holds the knowledge of all previous Graveminds. He also looks pretty cool. Since he's a part of my favorite Halo faction, that makes him my favorite villain
Prophets but the gravemind is also really good
Prophets
Prophets and Gravemind were cool. The fanatical leaders of a strict covenant and complete mastermind of the flood. They were kind of uncompelling though; they never had a moment were I could relate to their cause in any small amount. I mean, that is okay if a deep antagonist is not necessary. This makes it easier for a player to actively wish these villains to fail. What makes a villain fun (in my opinion) is their relatability. The causes they back, how they react, and how I may feel the same way i.e. "humanizing" them. For instance, the Arbiter is a great example.
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Tartarus was one of my favorites despite being off to the side.
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Tartarus, for sure. Yeah he was kinda of one note character but it worked for Halo 2 narrative.
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In my experience as a writer, I have discovered that a good villain is made when you are able to sympathize with them. The Prophets and Ripa Moramee were just radical, Tartarus was a sociopath swayed by lies, and the Gravemind was just pure, unadulterated evil. Don’t get me wrong, all of these characters were top notch villains, but here are my top three:

3. Atriox
At first, you are made to think that Atriox is just an angry Jiralhanae that has a passion for blood sport, but his backstory reveals something more tragic. He hates the Covenant for what they did to his pack. They sent them to die over and over and over again. One day, as anyone would, he snapped, and the best part is, you can understand why. I would have him higher on the list, but unfortunately we haven’t had much time with him. Hopefully he’s developed in more in future games.

2. Guilty Spark
Guilty Spark is a poor sap who is just trying to follow orders. Activate the rings, contain the Flood. Unfortunately, this big green dude keeps getting in his way, and destroying the thing he’s supposed to protect and curate. Oh, he killed Johnson? Wouldn’t you? The man is about eliminate your sole purpose in life. Sometimes drastic measures need to be taken.

1. Didact
“The Mantle of Responsibility for the galaxy shelters all, human. But only the Forerunners are its masters.”
-Ur-Didact.
The Didact began as a simple Forerunner Warrior-Servant, doing his best to assure his people’s place in the universe. I mean, of course the were the Reclaimers of the Mantle. They were the most advanced beings in the galaxy. The Flood are a threat, yes, but the shield worlds will ensure his people’s safety. Now the Builders are proposing what? To create an array of weapons to eliminate all life in the galaxy? What good will that do? That will only lead to the fall of the Forerunners! He built the shield worlds anyway, knowing his plan was the most effective survival tactic.
Now, put yourself in his shoes, your people think you’ve gone mad. Your own wife has betrayed you. You are just doing what is right for your people, but instead your are being imprisoned.
When the Didact was released, he learned that his people were all but extinct, and these humans were now taking up the Mantle. This revelation, combined with his millennia of silent rage filled contemplation, has now thrown him over the edge. He calls up his only allies, the Prometheans who once served him, and a practically useless bunch of species who consider him a god, and use them to assure you, the last Forerunner, your rightful place.
Yet, you are still defeated. Defeated by an Ancilla, a human, and an impression of your lost love, tasked with stopping everything you’ve worked for.
This is injustice.

The Didact hits number one for me, because in his mind, he is trying to do the right thing, and everyone he is sacrificing for is against him. You can hear in his voice and occasionally see on his face the pain he experiences, and the books make that even more apparent.
I agree with all of this.
Just the sheer power and ruthlessness of the gravemind has to do it for me. Just the idea that he is a collection of so much knowledge and power is very intimidating. And I dig it. I also liked the Didact, His story was interesting, but the game didn't make him really a big bad, but I think extended lore does do him justice if you're into that stuff :)
The prophets and the didact for me are the villains who give a reason to hate humanity, one very silly and another that leaves you wondering for a few moments, knowing that the Flood is the greatest threat in the galaxy. But there is clearly the superiority for being a superior species in the case of the didact.
Elite Honor Guards.
The gravemind was always intriguing to me.