Ambiguous Clone Ending

"Gwen Stacy Clone: But - are you sure - that you're - Spider-Man: Oh, I'm the real one, Gwen. Believe me. Gwen: But...how can you tell? Spider-Man: Simple. I...uh...Far out."

At some point in the story, the hero was cloned. At the climax of the story, the hero fights their clone and one lives while the other dies. However, whether the survivor is the clone or the original is left uncertain. This usually leaves a lot of uncertainty and angst because the survivor fears seeing a Tomato in the Mirror, and may grapple with the guilt of essentially having murdered him or herself.

Compare Schrödinger's Butterfly, where whether the heroes escaped the Lotus Eater Machine is left in doubt. Shell Game is a prerequisite.

Anime and Manga

 * Happens to  in an episode of Ghost in the Shell: Stand Alone Complex 2nd Gig. Fortunately, the character in question is so minor that it hardly matters it the original lived or not.
 * Fridge Logic should sort out which is which when you consider the skills that go into being on the Major's squad, and that the doppleganger in question only took on the character's appearance. In reality, the fight between the two shouldn't even have been close but for some Hand Wave about  supposed ennui.
 * In Read or Die
 * Though if you pay really close attention,
 * The first Lupin III movie, Recap seems to be heading for this until the climax, in which When Inspector Zenigata shows up at the end to arrest Lupin,  but the inspector doesn't care.
 * In My Hero Academia, the villainous Twice has this as his backstory. His quirk lets him make duplicates of anything, and he can easily clone himself. Unfortunately, he did this so often, that he and his clones forgot who the real Twice was. They started arguing, and the argument turned violent, until most of them killed each other. Only one survived, and while he'd like to think he's the original, he knows the odds are very much against it. This self-doubt and questionable self-worth soured his personality, leading to his Start of Darkness.

Comic Books

 * Doing this ultimately led to the Spider-Man Clone Saga.
 * And, by extension, to the somewhat shorter Brand New May saga in the Spider Girl comics.
 * It happens in Lobo.
 * For a while there, even one drop of Lobo's blood would grow into a clone. Whenever this happeeds, the Lobos would team up to kill all of their enemies and then turn on each other. The lone surviving Lobo would be declared the "real" Lobo. Since it didn't matter to Lobo—or any of his clones—who survived as long as one of them did, and everyone else in the DC Universe tries to avoid Lobo anyway, readers didn't really care either.
 * Except for Slo'bo. See, at one point Lobo was de-aged to about fifteen and hanging out with Young Justice, and he died... and when all the blood-clones grew up and started killing each other (while everyone else, thinking he was dead, was very far away), one of them ran and hid. After the others were done, he came out and ran back to Earth while the new Lobo was off doing whatever, but he was too ashamed to be called Lobo anymore, so he took a new name.
 * In Dirty Pair: Fatal But Not Serious, both Yuri (Girly Girl of the Lovely Angels) and her Laser Guided Tykebomb clone are seriously wounded while escaping a supernova. In the epilogue, one Yuri is bedridden as her partner Kei tells her about the funeral for the other Yuri she just came back from.
 * An odd case occurs in a The Incredible Hulk story arc where the Hulk is cloned. The final confrontation follows all the conventions of the Ambiguous Clone Ending: Banner and the Clone face each other alone, the fight itself isn't shown, and the scene skips to Banner returning to his friends telling them the clone is dead. It seems like we're meant to be unsure that the real Hulk won... except that the clone was heavily modified, and in Hulk form looks unmistakably different from the real Hulk. Since we see the Hulk looking perfectly normal the very next storyline, he's clearly the original... so why does the narrative go through all the plot points associated with this trope?

Literature

 * The end of the Alex Rider novel Point Blanc, ..Until the sequel came along, of course.
 * See the WMG which ties the more dramatic plot to the fact that Alex's clone won the battle.
 * Android at Arms by Andre Norton.
 * Subverted in Legend of the Five Rings. During the original Clan War story arc, Bayushi Kachiko uses an Artifact of Doom to create an evil duplicate of Doji Hoturi as part of her revenge against him for killing her son.  Hoturi finally faces the False Hoturi in a duel alone and away from any witnesses. But since the loser melted into goo and maggots upon death, it's quite clear that the real Hoturi won.

Live Action TV

 * Something similar, the Red Dwarf episode "Out of Time". Starbug is confronted by Which ship won isn't revealed until the next series.
 * Well, this isn't exactly a case of actual clones, but alternate universe doubles, but in one episode of Sliders (titled "Post Traumatic Slide Syndrome"), the characters find themselves on a world that's just like their own Earth, but with only a few differences. One of those differences is that that world's Professor Arturo missed the opportunity to go sliding through other dimensions with Quinn Mallory and the others, and has regretted it ever since. This world's Arturo gets in a fight with the regular Arturo just as it's time to slide. Before the portal closes, one of the Arturos leaps through and joins the other Sliders while the other is left behind. It's never made clear whether the Arturo who joins them at the end is the same one they started with.
 * Would the other Arturo have made a Heroic Sacrifice for Quinn?
 * The other Arturo was a jerk but he wasn't evil. Plus he could have Become the Mask.
 * In an episode of Psi Factor, a main character thinks his resurrected wife is actually possessed by an "Ancient", so he banishes her and resurrects her again. The ending heavily implies that it's still the same Ancient...
 * Played with in the third season of Farscape: after John gets "twinned", both characters are essentially seen as equally real and valid..
 * D'Argo and Chiana are also "twinned", but their doubles are killed during the same episode. They are both seen to be grappling with questions of "What if that was the real me and I'm just a copy?"
 * In the Downer Ending of the Are You Afraid of the Dark? episode "The Tale of the Chameleons", the Chameleon turns into a clone of Janice, and Sharon must decide which one to spray with water. She picks the real Janice, who is turned into a chameleon and drowned in a well, while the clone has plans to turn Sharon and her family into chameleons as well.

Video Games

 * In Kagetsu Tohya, if you decide to search for the killer, sometimes you do battle with him. The killer is you, somehow (I know how, but that would be spoiling). During some of the battles, it gets so confusing the fighters themselves begin mixing which is which, and the winner himself doesn't know who he is anymore. Try Again!
 * In Tales of the Abyss' ending, there are some indications suggesting is the one at the end, but the optional "Contamination Effect" sidequest has Jade suggest that  may be the one to survive. Other fans regard Mr. Ending as a combination of the two (something the Japanese OP lyrics may point towards).
 * Star Wars: The Force Unleashed 2 lives on this. In short, the protagonist dies in the canonical ending of the first game and is then cloned by the beginning of the second. The clone was imprinted with memories of the original up until to some point, essentially making him the same person. Midway through the game confusion arises when another character states that it is impossible to clone a Jedi (although Star Wars Expanded Universe has it possible, they just wind up crazy and evil). Then more clones of the original are revealed, going mad from their conflicting personalities, which you have to fight. And while the Light Side ending is pretty straightforward, the Dark Side ending is a guaranteed Mind Screw on the first playthrough: the main character is killed by another clone of the original, who succumbed to the Dark Side. It is implied that he exists in the Light Side version of the game as well but does not attack you because of your actions. And then the bonus cinematics hint that you already played as a clone in the first game...
 * The protagonist (of the second game) himself believes himself to be a clone, and at one point (at least in the novelization) refutes Rahm Kota's claims that Jedi cannot be cloned (at least not without physically degenerating) by pointing out that is as far as he knows. While the game and the novelization are deliberately vague, the supplementary material tend to state that he is a clone. The unlockable Distant Thunder, which detail the Dark Apprentice's training, feature Darth Vader displaying Galen Marek's corpse to the Dark Apprentice. Since the cinematics occur before the game's ending, and have no impact on the game's events themselves, and due to the fact that Databanks and a Force vision (in the novelization) confirm the existence of the Dark Apprentice, it is probable that Distant Thunder is canon, which means that the second game's protagonist is, in fact, a clone.

Web Comics

 * Occurs in Planet Zebeth between Samus and her backup.

Western Animation

 * One episode of Time Squad had Larry make a double of himself, with each double making another until there were hordes of them. Otto and Tuddrussel decided to shove all but one who claims to be the original into space. Despite the final Larry booted out being especially insistent he's the original and the one left behind giving an evil laugh, status quo is restored when he's shunted back to a subservient role.
 * Part of a throwaway gag in an Imagine Spot on Family Guy. Except that it was a Robot Replicant instead of a clone.
 * Played straight when Stewie creates an evil clone of himself.
 * Then subverted again when Chris thinks he has to either shoot Peter or an old man. This being Chris, he's completely ignoring how neither of them look anything alike!
 * One Halloween short on The Simpsons involving a magical hammock that made multiple Homer Simpson clones ends with all the Homer clones being sent plummeting down a cliff.