Doomed Protagonist

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"When I am taken, all my memories will fade, crowded out by eternal suffering. My imagination takes over and I see myself struggling through the body of the King, wracked with agonies and unable to remember any other existence. I know that I will have no more thoughts of freedom or safety or home because my very understanding of the concepts will be lost to me and it hurts. it hurts it hurts it hurts it hurts it hurts it hurts it hurts it hurts"

—The protagonist of Yahtzee's "The Expedition"

Let's say a character comes across something that Was Once a Man and, after discovering the source of The Virus that made it that way, looks in the mirror to find that he shows all the signs of being infected with it. Cue "Oh Crap." Roll credits.

Or the character learns that everyone who has come before him to a certain place, looked at a particular Brown Note, or performed a certain action has suffered a horrible and irreversible fate. Alternately, their death may be assured by getting lost at sea, locked in an airtight coffin, seriously injured or catching/developing an incredibly deadly illness or disease.

Either way, we know he's screwed. And unless he can Find the Cure, fight off his fate or have some miraculous Deus Ex Machina save him, all he can do is sit back and wait to die. In most cases, he's not going to find the cure or get rescued. (Except maybe in Fanfic. By aliens.)

The story almost always ends just short of his final transformation or death, and sometimes begins with a later scene that shows him doomed. It is also almost always told from the first person. These stories are usually Apocalyptic Logs.

This may happen because of a Viral Transformation, The Virus or The Corruption. Compare Tomato in the Mirror, when the character was that way all along. Contrast And Then John Was a Zombie, when this is used as an ending twist. Also compare Heroic Willpower, which particularly special heroes can use to resist their fate. Not related to Doomed by Canon or Foregone Conclusion, although they can cover protagonists who are doomed. May lead to acting like a Sheep in Wolf's Clothing.

Since this is a form of foreshadowing and an Ending Trope, spoilers abound.

As an Ending Trope, Spoilers ahead may be unmarked. Beware.

Examples of Doomed Protagonist include:

Anime and Manga

All the kids in Bokurano, due to the way that mecha battles in this series generally work -- if you win, you die. If you lose, everybody in your universe dies.
In Puella Magi Madoka Magica, the magical girls are doomed to become witches -- if they don't die first.
Seita from Grave of the Fireflies: The first scene is him dying in the streets and then it flashes back to the past.
Hibiki of Senki Zesshou Symphogear is going to die. The opening scene of the show is Miku visiting her grave. The rest of the show is functioning as a How We Got Here to this. And then it's subverted when we get past that point.

Comic Books

The comic version of Sin City: The Hard Goodbye shows Marv realizing that he was going up against the Roark family: a powerful crime family with many connections and no morals. Marv realizes that he's as good as dead but soldiers on anyway. He even surmises that he'll probably end up strapped to the electric chair, which is his inevitable fate.

Film

The premise of the classic Film Noir D.O.A. and its 1980s remake.
The heroine of The Ring (the U.S. version at least), when she realizes that she only has a few days to live after watching the tape.
District 9 plays with this trope. It may not be the best example, since the the moment of realization occurs halfway through the film, and no one prior to Wikus had experienced it before. However, it definitely counts.
Seth Brundle of The Fly.
This is the premise of Crank. However, it's subverted, as he ultimately survives.
Seven Pounds, in a rare, self-inflicted version.
In The Wrestler, the protagonist collapses due to a heart attack and his doctor tells him in no uncertain terms that he has to stop wrestling or he will die. But after he messes things up with his daughter, wrestling is all that he's got.
Godzilla in the film Godzilla vs. Destoroyah. He dies of nuclear meltdown due to radiation overdose.
The original ending of The Crazies remake had David getting a nosebleed, this showing that both he and Judy were actually infected with Trixie.
Everyone in Threads. It doesn't look like humanity, at least in the UK, will last beyond a few generations.
This is the very idea behind Jean-Pierre Melville's Le Samouraï, but in a simple crime drama. You know what's coming. And so does he.
Final Destination is basically Doomed Protagonists: The Movie Trilogy.
The title character of the movie Simon Birch is going to die. You know this from the beginning, as the First-Person Peripheral Narrator is narrating the entire movie over his grave.
Alien 3 has Ripley with a queen's embryo inside her. Granted we learn this approximately halfway through.

Literature

Commonly used by H.P. Lovecraft, for example, his story The Shadow Over Innsmouth may count. In the very end the protagonist realizes that he shares ancestry with the people of Innsmouth, and is destined to eventually turn into a Deep One.
The House on the Borderland by William Hope Hodgson
Several stories by Clark Ashton Smith including: The Double Shadow, Genius Loci, The Vaults of Yoh-Vombis, and The End of the Story.

New Media

At the end of the uncensored version of SCP-835's uncensored after-action report, it's revealed that the hero has been infected with The Virus and will soon go into containment with the other victim.
Two of Yahtzee's Fully Ramblomatic stories, The Hopeless Endeavour and The Expedition, end this way: one with the main character discovering that he's the latest in a series of thousands of clones infected with a terminal disease that will kill him within a few days and cause him to be replaced with another clone and the other with the main character becoming a prisoner of Chzo.

Video Games

Damn near every playable character in Eternal Darkness. Which, you know, is inspired by Lovecraft, so...
Shirou during the Heaven's Feel route in Fate/stay night, after having his arm removed by the Shadow and getting Archer's grafted onto him. The Dangerous Forbidden Technique that comes from using it would be survivable (though with a reduced lifespan) if he had years of gradual training to ease into it and did not have to overuse it—unfortunately, he hasn't got the luxury of either. Whether this is a subversion or not depends on the ending; in the True End, he gets better, in the Normal End, he doesn't.
- The prequel, Fate/Zero has this happen to Kiritsugu, who is cursed by the Grail, and dies a few years later, before Fate/stay night begins.
The Legacy of Kain series has Raziel. Pain, betrayal, torture, humiliation and death? Oh yes, he has that coming in spades, but his is a more brutal kind of doom: After being executed by his master Kain, he's resurrected as a soul-devouring entity. Later, he becomes bound to a spectral blade known as the Reaver. After travelling back in time he learns that the Reaver is in fact the soul of his own future self, once imprisoned within the blade and driven insane after millennia, and that it is his destiny to suffer the same fate.. He resists at first, but by the end realizes it has to happen and accepts it.
It looks like Rockman Trigger will remain stuck on Elysium. He's been up there for over a decade, and all of Roll, Tron's, and Capcom's attempts to bring him back to Terra have failed.
Resistance 2, where Hale has indeed been corrupted by The Virus, and fully transforms at the end.
Might be the fate of the two lead protagonists in Dead Rising. even the fate of the survivors are in question, well in Otis' opinion anyway. Also, at the end of the "real" ending, the message "And yet he complained that his belly was not full." is shown.
In Halo Wars this is the fate of Sgt. Forge when he enters the sun's core of the shield world.
Breath of Fire: Dragon Quarter. About thirty minutes into the game, protagonist Ryu is "infected" with the dragon power. At no point in the game does he even think about trying to find a cure or a way of fixing his condition. You do the math. Then subverted in the final cutscene when, at the end of his life, Ryu is granted a second chance by Odjn.
Dragon Age Origins. At the end of the game just before the final battle, you find out that in order to kill the Archdemon, a Grey Warden has to strike the final blow and will die in the process. You can choose to sacrifice yourself or ask the other Grey Warden in your party to do it, or Take a Third Option.
- The joining ritual that the wardens undergo is itself a death sentence. You die 30 years or so later, as your body finally succumbs to the taint.
  - Although everyone does die eventually, and in a society like theirs, most people wouldn't live much longer than that anyway.
  - Avernus would love to prove you wrong, as he's, pardon my words, old as shit AND a grey warden who's prolonged his life using blood magic.
Nearly every ending in G-Darius ends this way. Even the best ending is a little ambiguous.
A couple of R-Type Final‍'‍s endings leave the pilot disabled and floating in space.
Persona 3 ends this way. All the heroes know that it is futile to fight Nyx Avatar. Sure enough, after fighting it, The Battle Didn't Count. Shouldn't be all that surprising because it's a Mega Ten game and "Memento Mori" shows up quite a bit in the intro. It's ultimately subverted by the protagonist making a Heroic Sacrifice to contain Nyx Avatar.
Final Fantasy X. At first, Yuna is doomed as were all the summoners before her to become the next Sin after the calm. Once the cycle is broken, Yuna is no longer doomed, but it becomes clear that Tidus is now doomed because he only exists as a dream of the Fayth and will fade once Sin is destroyed and the Fayth awaken.
The ending to Diablo.
The Nameless One is damned even in the best endings of Planescape: Torment. Somehow it's not a Downer Ending, as Nameless is at peace with himself, and battling in the Lower Planes is old hat to him by now.
- And you've worked for that damnation almost the entire game - the quest for your mortality (and death) began right at the end of the first "dungeon". On a happier note, depending on who you have with you at the end and whether they survive said end, they promise to come for you.
The protagonist of Heretic 2 contacts incurable virus early in the game and is looking for cure (and the source) for the most part of it.
At the end of Metal Gear Solid 4: Guns of the Patriots, Old Snake, having survived fighting numerous Metal Gears, walking through a microwave chamber, and fighting Liquid Ocelot, knows that he only has about six months to live before his artificially accelerated aging finally kills him. But it's okay, because he's happy.
In Corpse Party, even if one avoids all the Wrong Ends and follows the True End path, four of the main characters die, along with a plethora of other victims.
Final Fantasy XIII-2: Serah. The game also reveals that all the player characters except Fang and Vanille were supposed to be this for the previous game.

Western Animation

One episode of He-Man and the Masters of the Universe (2002 version) tells the legend of King Greyskull, He-Man's predecessor. An oracle predicts he will not survive the battle against Horak, but he heroically confronts the villain anyway sealing Hordak and his dark army away before succumbing to his wounds.