- The creature Omega is a reoccurring super-boss in many Final Fantasy games. Originally it was just a powerful machine that, according to Final Fantasy lore, would just randomly attack things that got near it. More recent games and story expand on Omega's back-story and imply that the different versions of Omega in other Final Fantasy games are in fact the same thing and Omega really exists across multiple universes with a shape that conforms to the laws and rules of said universe. Also, one story states that Omega is supposed to kill a powerful foe whom most assume to be Shinryu, a powerful god-dragon that also exists across multiple universes. One of the game quotes for this this thing is: "From the sky it comes, heartless and bloodlessOmega, Bringer of the End! Unleash your might in the name of destruction... and may all men know despair!"
- The Cloud of Darkness, the Final Boss of Final Fantasy III looks like a tower-sized, green, naked woman with tentacles, but it is in fact the Anthropomorphic Personification of Primeval Darkness, transcending time and space and threatening to engulf everything, under A Form You Are Comfortable With. Later games scale it/her down as a Humanoid Abomination though.
- Zeromus, the final boss of Final Fantasy IV, is a spirit of hatred created by the true Big Bad of the game, Zemus, when he is killed by Fu So Ya and Golbez. He literally exists to consume all life, and first appears as a spirit that can't be harmed, but once the Crystal is used on him, he transforms into a being that would make H.R. Giger proud.
- Exdeath in Final Fantasy V. He just plain is the part normally and really looks it in his ultimate Tree form at the final battle and as Neo Exdeath. He was born from an aggregate of evil souls sealed into a sacred tree, and later becomes an embodiment of The Void.
- In the cave leading to the Fire Tablet (found under the ocean, naturally!), there are a number of creatures that are piles of...organs, skulls, and vile expectoration. They are simply called "Unknown", with no distinction between the different versions.
- Jenova of Final Fantasy VII is an Expy of the creature from The Thing (1982) and conceptual sibling to Lavos. Jenova has no set form, and mimics the appearance of its prey; in this case, the vague outline of a woman, with missing limbs and eyeballs in place of nipples. Its descent marked the downfall of the Cetra civilization. By extension, Sephiroth - the fruit of a project to create Jenova-infused superbabies - is half-human, half-Eldritch Abomination.
- The WEAPONs are Antieldritch Unabominations. In the backstory of the game, these creatures are the all-natural guardians of the Planet/The Lifestream (your mileage may vary if the Lifestream can count as an eldritch entity). Unfortunately, humanity has proven itself dangerous to the Planet, so they went aggro on human cities.
- The "Unknown" return in the crash of the Gelnika as bizarre, sometimes-flying, obscenely powerful creatures.
- Xagor of Final Fantasy Legend III, which resemble nothing more than a mass of flailing tentacles and fanged mouths.
- In Final Fantasy VIII, Big Bad Ultimecia becomes this under her One-Winged Angel form. A building-sized, multi-coloured, symetrical, mishapen, grotesque... thing, with a black void with a flickering light for a face and a starry night inside of her "gown", who unravels and absorbs the whole space-time continuum just by being there.
- In Final Fantasy IX, there is a superboss called Ozma. It may have once been an Eidolon, but now it's just an incredibly powerful swirling sphere of something.
- In Final Fantasy X, Sin is a giant monster the size of a city that emerges from the depths of the ocean to completely annihilate all settlements larger than small villages at random intervals and terrorized Spira for a thousand years. Even if it is defeated by a High Summoner, by sacrificing themselves and their friends, it returns a few years later by reincarnating from the body of the High Summoner's closest friend to continue its rampage. Sin leaves swarms of smaller monsters in its path and everyone who survives coming into contact with its toxins (fortunately) suffers from massive memory loss. And apparently, it can wipe out entire armies by causing distortions of space.
- The Fal'Cie from Final Fantasy XIII are bizarre mechanical-looking monstrosities with some sort of alien intelligence.
- In the sequel there's Gogmagog, an abomination that the above mentioned Fal'Cie had to throw out of the time-space continuum to be rid of.
- Final Fantasy Tactics A2 has the Neukhia, whose presence is so dangerously poweful, even having a LIMB in Ivalice presents an apocalyptic threat
- Chaotic Darkness of Final Fantasy Brave Exvius: a Vision of the darkness and evil hidden in the hearts of the people living in Lapis; its first appearance is a skeletal... thing, and its second looks like an amalgamation of various enemies you would have met in your travels. And summoned to prove that the world is evil and deserves to be destroyed....
Eldritch Abomination / Final Fantasy