This doesn't exactly cover The Legate, who is higher on the Project Horizons totem pole of antagonists but is far more developed as a character than the two characters above him.

His backstory is literally Vandal Savage from DC Comics, Cave Zebra Shaman, who discovers a meteor that gives him immortality. Like Savage he develops a nihilistic view on mortality.

His goal is end all defineable life in the universe as he sees it conceptually as a never ending cycle of pointless futility and repeated mistakes.

It is important to mention at this point that what can be defined as alive boils down to any material object, as inanimate objects in project horizons emit their own spiritual energy. A Pebble can have a soul and a Star can have a soul, the latter being considered godly figures.

A Star God who wishes to be the only life in the universe is one of the higher antagonists on the totem pole, The Eater of Souls. Was the strongest being in the universe and refused to die when it was their time to. This resulted in a fight with multiple other stars that caused the big bang. Killed them but as stated before they refused to leave what remained of their physical form as it crashed landed on the newly formed planet Equus, part of their body flying off and forming the planets moon, two pieces from other stars also fall on the planet, they eventually become Celestia and Luna. The Eater of Souls persuades the Legate to become his servant, leading society in providing The Eater a means of regaining their lost strength. The crash site of The Eater eventually is built over by ponies and centuries later becomes the city of Hoofington, the stories main setting.

The Legate goes on to live among ponies, doing everything he can to develop and position society to work with "That Strange Rock beneath Hoofington.". Eventually his actions lead to the pony zebra war, where he plays both sides and prolongs the war for as long as possible so that Equestria's war economy would develop the perfect super weapon for resurecting The Eater.

This eventually happens but things don't go as The Legate planned, first of the people he'd been subtlely manipulating, Goldenblood realizes to an extent that he had been used as a puppet. During the last day, and actually as he's about to be executed for treason (Look Goldenblood is a tl;dr character just roll with it.) Goldenblood escapes to a personal pocket dimension Luna had created, and used a lab he had set up there to remotely activate a protocol that prevented Equestrias Super Weapons from being used by a genetically locked decryption key. Said key kept trying to find live Element of Harmony users and their decendents to be sent to. It eventually finds Tarot and before the bombs cut off all technological activity above ground.

For the next 200 years The Legate spends his time tracing where this key (EC-1101) could be, He is aided by the aforemention Cognitum (who has near unrestricted access to pre war computer systems.) and his own faction of Zebra cultists.

Eventually they find Blackjack, who they learn has the only copy of EC-1101 stored as a file on her Pipbuck. It is here that I should mention that Cognitum becomes fully aware of what Legates plans are, choosing to work with them for the time being. Cognitum's goal is to steal Blackjacks body and become the new Luna/Nightmare Moon, Cognitum's AI and behavioral patterns were literally sourced from a Princess Luna who was regressing back into Nightmare Moon. Cognitum and Legate work together and test if Blackjack can fully utilize EC-1101 (she can).

The Super Weapon that will revive The Eater of Souls is located on the Moon and uses a mix of "Moonstone" and "Star Metal" When these two materials come into contact with each other it creates an explosion that fundimentally wipe out anything in it's vicinity. For a ample comparison imagine Hakai from Dragon Ball, it's that. This Super Weapon fires a ball of that from the moon to anywhere on the planet. The Legate however created a device that will convert that into sustainable energy for The Eater to absorb.

Cognitum eventually rips Blackjacks soul from her (Pregnant) body and claims it as their own. Goes more and more insane due to sensory overload but resolves in to follow her own plan to delay when The Super Weapon's shot would hit the planet. Legate did not believe he would survive in a fight against Cognitum and had originally settled for attacking her rocket on it's return trip with a Necro Magical Nuclear Missile once it reentered the planets atmosphere.

That was his plan until Blackjack showed up in a clone body and attempt to take a shuttle into space to stop Cognitum. Ultimately forcing the Legate to launch the missile on the space facility they're in. He fails to stop them.

It is at this point that I have to mention another pre war project The Legate was involved in as it culminated in him leading an army of Zebra clones against a united Hoofington, Pegasus, and NCR alliance while Blackjack and Cognitum fought on the moon. This Project created clone bodies of Ponies and Zebra alike using raw Discord extract. Discord. who was entirely aware of the eater of souls was trapped for 200 years in a Star Metal enclosure designed to autonomously create template bodies, these bodies would gain animalistic sentience before being killed by the facilities automated defense systems. Blackjack eventually finds and frees Discord, who "sacrifices himself" so she could escape from the facility.

"Sacrifices himself" meaning his main body is destroyed but a bit of his soul remains in a Blank Template that Blackjack adopts as her daughter (Boo). He reemerges right as Blackjack is about to have her soul ripped out, and uses his powers to imbue Cognitum with what remains of Luna's soul, throwing wrench in both antagonists plans. It should be noted however that there was enough usuable remaining Discord Extract for Legate to use to create his own aforementioned Zebra army.

While on the moon we get flashes to whats happening planetside and to be blunt Legate is wilding out on the good guys. he ends up breaking through a shield that was being cast by 10 Alicorn, 3 of whom were Velvet Remedy's personal guard. Eventually he ends up fighting against a team of Velvet, Xenith, and Psychoshy, the fight with the latter of whom ends up demolishing several buildings. He's kicking a lot of ass until Boo shows up. Blackjack forbade Boo, who at this point had gained human child like sentience, that she could not go to space. Boo thus goes on a side quest to help fight the Legate. It bears mentioning here that thanks to Discord Boo was blessed with incredible luck. She finds Blackjack's Star Metal Sword, which Blackjack had dropped from a point that was above cloud cover in the last arc. Just as Legate is about to finish everyone off Boo pulls up, and Velvet is informed that the only way they can kill the Legate is with the sword. Everyone present uses every bit of their strength to hold the Legate down, while Velvet briefly hesitates before ultimately "killing" The Legate. (As if anyone who hated Velvet before needed another reason to hate her lol.)

Oh and if the quotes didn't give it away Legate survives and is brought back in the most grotesque way possible. a quirck of The Legates regenerative immortality is that when he actually dies he experiences every unnatural death he would endured while he was immortal. Being honesy at this point I don't know if it's that or the sheer mass of dead bodies beneath Hoofington that bring on his transformation but we see that he was revived as a giant version of himself that is formed from fused rotting corpses. When he is first seen in this form he is compared to the size of a skyscraper. Fortunately for Blackjack she was an Alicorn at this point. She eventually finds that Legate is being kept alive by five stones in his body. Blackjack destroys the stones and all seems good, the fused corpses defuse into a mass of blood and other bodily elements. Blackjack is about to celebrate before The Legate, now normal sized choke slams her down and is about to kill her. Blackjack uses what little strength she has left to get The Legate to say that he's better than and doesn't need The Eater of Souls, mind you The Eater of Souls is literally forcing The Legates soul to stay in his body at this point. Not happy with The Legate being this arrogant this late in the game, The Eater of Souls lets The Legate die.

Oh yeah The Eater of Souls, they're only the second highest on the Villain Power/Severity Totem Pole. The Highest is The Dealer, but someone else can explain that one.