"Never bring Time Travel, the Cthulu Mythos, or Giant Robots into an established setting, because if you do, all it will ever really BE about from then on, is Time Travel, or the Cthulu Mythos, or Giant Robots. Or Giant Robots traveling through time to fight the Cthulu Mythos."
Well, this summer has been one headlong dive into whirlwind romance for me. Ha! I wish! As You Know, I've spent most of the summer trying to run into Percy Marlborough (sigh!), the handsome young industrialist I met the day I snuck into the country club on a lark.
OH GOD OH GOD OH GOD. He's not human.
If anyone finds this, I beg you, call the police. Tell them our city is full of insect-lizard creatures that walk invisibly among us and feed on our emotions, an ancient eldritch race that see all our efforts and strivings as the caperings of monkeys."
Final Fantasy IX. The final boss is Necron despite Kuja being the main antagonist throughout the game.
In Persona 2 Hitler turns out to be Nyarlathotep in disguise.
In Mass Effect, you're initially in pursuit of Saren, a secret agent bent on using synthetic organisms to wipe out humanity. Surprise, he's really working for the Reapers, an ancient race of machines who have wiped out all galactic civilizations several times over.
The Chzo Mythos does this at the midway point: The first two games were straight slasher horror stories with the single central antagonist, but starting with Trilby's Notes the series' focus shifts to the Cosmic Horror possessing the previous games' antagonist, the titular elemental god of pain. (This is because Yahtzee was making up more story elements as he went along.)
Not the main plot, but Oracle Of Tao has a bounty hunting sidequest that is relatively calm and relaxing, until you get to about the last monster, who turns out to be an Eldritch Abomination. Losing the battle against this last bounty results in a Mind Rape ending. For a Side Quest, this is still pretty heavy... and there are actually a number of these practically immortal destructive beings roaming about.
It was known that the Halo rings were built to kill the flood (or more precisely, their food—which is essentially all life in the galaxy— and starve them out) since Halo 1. The Eldritch Abomination Gravemind however didn't show up until Halo 2, so they were more or less space zombies until the giant iambic-pentameter speaking venus flytrap came onto the scene. And it should be noted that the Flood shifted the focus from a war with Scary Dogmatic Aliens to themselves.
The Gravemind turns out to be behind prehistoric galactic mysteries like the disappearance of the Neglectful Precursors, similarly to Mass Effect, though. I mean, the Gravemind is able to corrupt Cortana...the AI. That's a pretty scary thing for an organic being to do without using a computer. But the fact that it is basically, recognisably, definitely a biological organism as we know them rather keeps it out of the Eldritch Abomination category. :P
Assassin's Creed is a perfectly normal game about an evil organisation forcing the PC to relive the genetic memories of his ancestors, tied in to an ancient-evil-conspiracy plot. Suddenly, Abusive Precursors arrive and the world's about to be destroyed by some sort of horrible thing.
This has happened to Eggman how many times now? That is, the point is that Eggman suddenly finds himself out of his league when his schemes provoke godlike horrors, such as Perfect Chaos, Dark Gaia, and Solaris, and Sonic has to go Super to bail Earth—and Eggman—out of the mess the doctor had caused.
Towards the end of Romeo X Juliet, it becomes clear that the true enemy isn't the murderous Lord Montague, who is slowly descending into cackling, city-burning madness, but rather the death of Escalus, which is what's holding Neo Verona in the sky: the earthquakes that become much more frequent and ruinous towards the series' climax are the result of Escalus slowly perishing.
Gonna have to put Digimon Tamers in here, considering how the D-Reaper turned it into this.
The Cabin in the Woods would also be a good example for this trope, with the run-off-the-mill horror/slasher story being revealed as a setup to please the Old Gods slumbering below us. They're not cosmic though, they just "ruled the earth before man".
The World's End begins as a story of five childhood friends reuniting for a pub crawl in their old hometown. They struggle to come to terms with their problems, their friendships, and their pasts. It's a strong character development piece that gets hijacked about halfway through with the sudden revelation that the townspeople have been replaced by alien robots.
The first three books of Venus Prime are about a young female detective who solves mysteries in space while trying to discover The Conspiracy that caused her to lose three years' worth of memories. In the fourth book, she pretty much wipes out the conspiracy. And then, suddenly, the Starfish Aliens start to show up, and the rest of the series is about her and her allies trying to prevent one faction of the aliens from attempting to re-write history so that Earth becomes more like their homeworld - which would make it uninhabitable to humans.
South Park: The episode "Pinewood Derby" begins with Stan competing for the derby and his father Randy cheating to win, which catches the attention of cosmic beings who subject humanity to a morality test.
Five hats means that five tropers think it is ready to publish.
You are saying that you think this draft is ready to be published. That means the description is not ambiguous,
it doesn't duplicate an existing trope, there are at least three examples, and the title makes sense.
Is that what you meant to do?
You are saying this draft has a ready-to-publish hat it does not deserve and you are taking it back.