Pokémon 2000: Ash is the chosen one. It became a meme for him to be the chosen one of everything.
Sailor Moon: the title character, and to a lesser extent, all the other "Sailor" characters...the non-evil ones, at any rate.
In Tokyo Mew Mew, the creation of the eponymous Magical Girls is initially presented as an accident, but even with LEGO Genetics in place, the whole thing seems too convenient. Near the end, Mission Control reveals that they were lying and had actually gone and tracked down five girls that were perfect matches for the DNA they had lying around. It's explicitly stated as the Earth itself having chosen the five of them to protect it.
Subverted in Flame of Recca where it turns out that the hero is NOT the chosen flame-wielder, and the villain IS.
Magic Knight Rayearth: Three schoolgirls are dropped into an alternate reality where they are declared to be "the legendary Magic Knights" and are set off on a journey to become said legendary Magic Knights.
Heavily subverted in that what you (and they themselves) think they're chosen for and what they're actually chosen for are in no way close.
To clarify, they were tasked to "Save Cephiro" which is as pretty straightforward as it gets, since they were given the name of the person who wants to stop them from doing so, and said person is actively trying to stop the heroines. They were never informed who they were supposed to save Cephiro from.
Naruto: It is revealed in part 2 that Jiraiya was told one of his students would be the one who would either destroy the world or save it. He originally thought it might be Pain, but before he dies he thinks it might be Naruto instead. Later Tsunade also refers to Naruto as the child of prophecy.
Actually, both Pain and Naruto are "Child of the Prophecy". Jiraiya was the one who determined which would decide the fate of the world. And later event's imply that it was originally referencing Minato and Pain, before Minato dying and passing it onto Naruto.
Kamui in X1999, as well as the rest of the Dragons of Heaven and Earth.
Griffith of Berserk is a good example of a villainous Chosen One, what with being chosen by the Crimson Behelit to become the fifth member of the Godhand during the Eclipse.
Goes even further than that. He's the chosen king of the midlands
Played with in Neon Genesis Evangelion, where Shinji is one of the half-dozen or so people on earth who can defend humanity...and still manages to be a whiny, insecure loser. He, Asuka and Rei are rewarded for saving the planet by having...dinner at a Ramen restaurant.
Subverted and then played straight in Ichiban Ushiro No Daimaou right on the 1st episode where the protagonist is calculated to be this generation's demon king. Six chapters later, Hiroshi is also shown to be sorted as the next Hero, and this is confirmed by taking on the legendary weapon.
Yu-Gi-Oh!: Yugi (the little one) is referred to as a Chosen One, though in this case, a more appropriate description might be chosen vessel as his body provides the spirit within the Millennium Puzzle with a physical connection to reality allowing him to save the world. Though Yugi turns out to be the one who will defeat the pharaoh in battle allowing him to move on to the afterlife. Yugi tends to have more messianic associations to his name than Yami Yugi.
In its various continuities, Digimon has two distinct categories of humans partnered with Digimon, the first and most well known falling under this trope. The Chosen Children (dubbed as "Digidestined") are chosen by some higher power for the purpose of partnering with a Digimon to save the Digital World. The term is explictily used in reference to the protagonists in Digimon Adventure and its sequel (who are picked by the members of Gennai's order), and Digimon Frontier (where Ophanimon is the one who chose them). Unlike most examples of the trope, there are multiple Chosen Children, to the point where the Adventure continuity had an arc where the main characters assisted Chosen around the world and concluded with everyone in the world becoming one.
Yu-Gi-Oh! GX follows it's predecessor, with Juudai being the Chosen One to protect the universe from the Light of Ruin. Johan is also apparently a Chosen One, but of what is isn't ever revealed.
In Eureka Seven, whoever makes a human Coralian smile first naturally makes that person "the chosen one". "The chosen one" will pair up with the particular human Coralian to lead humans and Coralians to co-existence and prevent war. The protagonist Renton Thurston was that very person, and the only one shown in the entire series to achieve things where no one else can. He wasn't "chosen" in the prophetic sense, but chosen by Eureka to be her mate. A bonus line for this trope, said by Maurice in the final episode: "The only one who can save our mama(Eureka), is our papa!(Renton)"
At the end of the anime, Madoka becomes a magical girl and uses her wish to keep witches from being born, though she ultimately Ascends to a Higher Plane of Existence because of it and renders herself Ret Gone because the wish would have transformed her into a witch herself.
Madoka Magica is a deconstruction of this and several other tropes Homura, one of Madoka's friends, has the ability to travel through time. When Madoka was killed (In Homura's timeline), she kept going back to stop her from dying. She failed repeatedly, causing numerous new time lines to form. These actions to prevent Madoka from becoming a Magical girl, inadvertently made her to become the chosen one, as so many timelines tied into her, her power greatly increased. She was chosen to be the great savior/destroyer because of Homura's actions
The Book of Darkness, an all powerful magical tome from Magical Girl Lyrical Nanoha chooses its master at random, and the most recent one is a paraplegic young Japanese girl by the name of Hayate Yagami. this also makes her a different kind of Chosen One, as Gil Graham, the TSAB admiral who had been tracking the book down decided that she will be the last master, as he planned to seal her together with the book when it goes berserk when it is completed since she was alone and nobody would mourn for her.
DC Comics has a Chosen One in the form of Billy Batson, chosen over everyone else on the planet to wield the powers of the gods as the mystically powered superhero Captain Marvel.
In the Doctor Who Magazine comic strip "The Glorious Dead", the power behind the Omniversal Spectrum intends to pass its power to one of two adversaries, representing good and evil. The Master believes the Chosen Ones are the Doctor and himself; they're actually the renegade Cyberman Kroton and the Master's Dragon, Cardinal Morningstar.
In Ultimate X-Men, Jean Grey is believed to be the reincarnated Phoenix God and is being fought over by two cults. It's deliberately ambiguous whether she is, or is just a very powerful mutant with a lot of mental problems.
Sonic the Hedgehog's sidekick, Miles "Tails" Prower, was named as the Chosen One in a prophecy made by the Ancient Walkers that said he would collect the Chaos Emeralds and begin the "Great Harmony." Though this fact has been tapped on numerous occasions, Tails has yet to bring about the "Great Harmony" prophesied.
Actually, he did, sorta — A.D.A.M. used Tails (in his Super Mode) as a focal point to gather together all the Chaos Emeralds in the universe on Mobius, where they were eventually thrown into the Special Zone and fused into a single set of seven.
Evil Dead: The comics go into much further expositions and machinations that revolve around just how much it sucks being The Chosen One. (Aside from all your friends and loved ones going deadite ) Makes sense seeing as The Necronomicon itself has its ties directly to each one of each generation. Even going so far as to have a Werewolf assistant type with his mentor's full journal account of the last generation's Chosen One who apparently worked himself into the Jack the Ripper mythos.
Spider Man is not a very powerful character by comparison with the people around him, but he has an odd tendency to discover there are ancient prophecies about him. He was, for instance, destined to stop the "Bend Sinister" (alongside Dr. Strange), and no less a pair of personages than Lord Chaos and Master Order claimed to have guided his life to defeat Thanos.
There is a Spider-Man story arc which explains that Spider-Man is the chosen avatar of the Spider God, and most of his villains are the avatars of various Animal entities as well.
Green Lantern: Particularly true in Alan Scott's case as he is the third Chosen One in a line with each being chosen for a different purpose. To a lesser extent, the Green Lantern Corps consist of 7200 members who are the "Chosen Ones" for their specific sectors of space (though they're chosen for worthiness, not to fulfill a prophecy.) The only true chosen one of the Corps to date is Sodam Yat who was tied to a prophecy about the Blackest Night.
Kyle Rayner, however, was a subversion. Ganthet gave him the last GL ring because Kyle was the first person he saw.
Subverted in the comic Chosen. After a series of unusual events, Jodie discovers that he has a greater calling, and is destined for big things. After saying goodbye to all his friends, Jodie goes off to fulfill his true destiny... as the Antichrist.
Zerain in Megalex. He's destined to lead the Undergrounder rebel tribes against the evil technocrats on the surface of the eponymous City Planet.
Kung Fu Panda has the fat panda Po chosen as the Dragon Warrior by Master Oogway, seemingly just for bursting into the arena via fireworks. Seen as a decision marked by senility and coincidence by his disciple Shifu, Oogway nonetheless genuinely believes Po is more worthy than any of the highly trained Furious Five. It takes a while, but everyone realizes that the turtle's choice is absolutely right.
The Lion King 2 makes use of this when referring to the cub Kovu, who was Scar's 'chosen one' as heir to the throne of the Pride Lands.
Film - Live Action
Neo in The Matrix. In Reloaded, Neo discovers that the One is a byproduct of the Matrix, anticipated and manipulated by the same artificial minds. Neo is just the latest of a long line. What makes him unique is his refusal to serve the function of the One.
In Star Wars, Anakin Skywalker is the Jedi's prophesied Chosen One, though he goes through several movies of being The Dragon before doing a Heel Face Turn and fulfilling his destiny. He remains extremely lucky and unusually skilled (at everything except relationships, apparently) the whole time, consistent with a standard Chosen One package.
Played with in the 2006 remake of The Initiation Of Sarah. The villains assume that the powerful Magical Girl Sarah is the girl of prophecy that they need to sacrifice to complete their evil ritual. It is actually Sarah's Muggle sister, Lindsey.
Subverted in Willow, where a baby girl is prophesized to be the one to bring about the evil Bavmorda's downfall, but what actually happens is that all the people trying to protect her end up defeating the evil queen while she's still a baby. This happens in no small part due to a healthy dose of Self-Fulfilling Prophecy on the Big Bad's behalf.
In The Last Starfighter, the eponymous hero has earned his way into the elite group of soldiers who are the last hope against the massive enemy fleet. However, he refuses the call and just wants to go home. On his way home, all the other soldiers are killed by a saboteur and he is forced to become the Last Starfighter.
In The Mummy Returns, Brendan Fraser is suddenly revealed to be the chosen one, even though the first film never made any mention of a prophesied chosen one, and every other character was a reincarnation of some ancient Egyptian/ninja. Same thing happened in The Chronicles of Riddick, but without the Egyptian/ninjas.
The baby boy in Legion is supposed to be the second coming.
The titular character in The Sorcerer's Apprentice is the Prime Merlinian, a sorcerer whose potential is equal to that of Merlin himself. Like Merlin, Dave is supposed to be able to do magic without a ring (or cane in Horvath's case). However, he lacks training in order to use this power and still needs Merlin's ring at first. He's also a physics genius, which is, apparently, a side effect of him being a sorcerer, and uses a combination of science and magic to defeat the Big Bad.
Katniss from The Hunger Games. Arguably, she chose herself when she stepped up to volunteer, but by the later books it's revealed that some of the other characters have gone to great lengths to keep her as the figurehead for the rebellion.
J. R. R. Tolkien's The Lord of the Rings is chock full of them: Frodo Baggins, Bilbo Baggins, Aragorn. Although it can look like Frodo chose his task by himself, both he and Bilbo seem to have been pre-destined to carry the Ring: "Bilbo was meant to find the Ring, and...[Frodo was] meant to have it." Word Of God has confirmed that Frodo's apparent 'choice' was accepting his destiny, and mentions that no-one except Frodo could have got the Ring all the way to Mount Doom.
Subverted, while Harry Potter is even given the "chosen one" title by the general wizarding public, though this is based on a correct guess anyway. Oddly enough, Harry is not chosen by destiny but instead by his nemesis - who, in his ignorant paranoia, makes a rod for his own back. Played straight in the way Harry fulfills the role and the way most people treat him throughout the books.
As much as the trope is subverted, it's also played out literally; Voldemort overheard a prophecy about a child who would/could destroy him, which might have applied to either of two infants. The ONE he CHOSE to go after was Harry, and the rest is history.
Though, it is also worth mentioning that the infant Voldemort didn't choose (Neville Longbottom) ended up playing a major part in his defeat (destroying the last horcrux) as well.
Also played with, in that Dumbledore states outright that he believes prophecies are only fulfilled if people want them to be, Voldemort chose to believe that only Harry could kill him, also implying that if Harry decided to say Screw Destiny anyone could have done it.
Inverted with Rincewind in The Light Fantastic, who learns that he was Chosen by the Eight Spells to carry one of them around in his head. Not because he's actually expected to do anything heroic or impressive, but because he's a coward who's good as escaping danger, so can at least be expected to survive until the spell is needed.
Subverted by Carrot. From the first book he appeared in (Guards! Guards!), it has been obvious that he was the Chosen One to be king of Ankh-Morpork: he was a poor farm boy, he's Lawful Good, he has a cool sword, etc. However, even though later books have made it obvious that Vimes, Vetinari, Carrot, and other members of the Watch know he is the Chosen One, Carrot prefers to remain in the Watch.
Brutha Small Gods. The trick here is that Brutha doesn't want to become the prophet, but is actually the Only One that believes in Om...
Also subverted in the later Discworld novel Going Postal, in which Moist von Lipwig is the Chosen One simply because he's the One who happens to be available. "At a time like this, any One will do!"
In the Wheel of Time fantasy series, Rand al'Thor is chosen by destiny to be Dragon Reborn. The previous Dragon was Lews Therin Telamon/Kinslayer. (The series hasn't said anything on who chose him, but, what with time being a wheel and all that...)
It's also a deconstruction. It's not just the taint that's making him insane, it's the knowledge that all of existence rests on his shoulders, while foolish people are fighting their savior at every turn. That much stress would drive anyone mad.
All the other main characters have their own role to play in prophecy, so he really shouldn't feel so alone. Though his role is more central, and he is regarded as the chosen one of several different prophecies, of whom the supporters of one still see little reason to cooperate with other people despite having the same chosen one.
In L. Ron Hubbard's Battlefield Earth, Johnny Goodboy Tyler is recognized as the one, the individual who almost single handedly defeated an empire of billions of beings on thousands of planets. He is even introduced to the alien ambassadors as a force majeure, an unpredictable and unstoppable factor whose coming changes the whole Multiverse.
Un Lun Dun by China Miéville subverts this. A book of prophecies says that Zanna is supposed to be the Shwazzy, the one who will save the world from Smog, the Evil Overlord. But when Zanna is injured, her friend Deeba must take up the fight against Smog, even though she's in the prophecies as the Plucky Comic Relief.
Subverted in Jonathan Strange & Mr Norrell where there is a prophecy about the two bringing magic back to England and they think of themselves as chosen ones, restoring magic to its peak, except that they don't match the Messianic Archetype at all (especially the unsympathetic Norrell). Additionally, their skills pale in comparison to those of earlier magicians, and in essence, they are pawns setting events in motion to hasten the Raven King.
In The Belgariad and The Malloreon, Garion (or Belgarion, his adult name) is the Chosen One (his actual prophetic title) who has to save the universe, kill the bad god, raise the new one, and keep control of his wife. And that is no mean feat. Then he has to do it all again in the sequel series.
This series takes this trope quite literally. The voice in Belgarion's head tells him that the world's reason for existence is to give him a place to stand when he achieves a Crowning Moment of Awesome.
Slight subversion with the Prophecy of Light: while Garion technically is the main Chosen One, the prophecy makes use of several others for various reasons. Driven home when the Prophecy itself informs Garion that what's happening with two of the others is, quite frankly, none of his business.
George R.R. Martin's A Song of Ice and Fire series seems littered with people who believe they are or who might be the Chosen One. So far, Prince Rhaegar, Rhaegar's children, Stannis Baratheon, and Queen Daenerys have all declared themselves or been declared by others to fit the prophecy. Fans also name Bran and Jon as possible candidates based on everything from their actions to possible parentage.
In a subversion of the trope, Daenerys and Khal Drogo's son is prophesied to be 'the stallion who mounts the world', who will unite the Dothraki tribes and lead them to domination over the eastern continent. However, instead the child is killed in childbirth by an evil witch a woman who wanted revenge on Drogo for the destruction of her village and the prophecy is thwarted.
One could argue the prophecy was meant for Drogon.
In The Naming by Alison Croggon, Maerad is specifically mentioned in the dream of a seer centuries ago and is foretold to destroy the Nameless One in his greatest uprising of evilness and save the world. She's also known as The One, The Fated One, and The Foretold. The series is not known for subtlety.
Sparhawk in the David EddingsElenium trilogy is the one destined to wield the mystical sapphire rose known as the Bhelliom. Eventually, this is explained by the fact that the Bhelliom, centuries back, actually spawned a human offspring, from whom Sparhawk is descended. Sparhawk is, essentially, a minor god and never knew it.
This is about the only thing he's destined to do, because he's Anakha, the Man without a Destiny - a trait that scares gods because, unlike any other person with a destiny, they can't predict what he's going to do from one moment to the next.
In the David Drake military SF series The General, Raj Whitehall is 'Chosen' by an ancient AI to save Human civilization on the planet Bellevue.
Followed up with several other Chosen, in several sequel series.
Seen also in Drake's later Belisarius Series, with the eponymous general (who formed, along with the 5th century AD Roman Empire he served in Real Life, the historical basis of The General) being chosen by Aide.
In the Malazan Book of the Fallen, there are several possible 'Chosen Ones', such as the deathless Rhulad Sengar who is chosen by the Crippled God to be the ruler of his mortal empire (but is then brutally and unexpectedly dispatched by Karsa Orlong using loopholes in the laws of magic). A better match may be Ganoes Paran, who is chosen to become the 'master of the deck', the arbiter of who will be chosen for godhood, for fairly obscure reasons. However, this power is not overused as he is only present in three of the eight published novels so far.
In an interesting switch, Ansurimbor Kellhus deliberately sets himself up as the eponymous 'chosen one' of The Prince Of Nothing through the manipulation of other characters, religions and factions, rising from solitary traveller to Emperor of the known world over the course of the series and its sequels.
If this editor had a nickel for every time someone said Sword of Truth's Richard was "the only one" who could do whatever needed to be done, he wouldn't have to worry about his student loans.
Every single main character in every single series in Warrior Cats. And now, as of Power of Three, they're getting special powers, too.
Actually, Squirrelflight, Leafpool and Stormfur (if his short time as a protagonist in Moonrise counts as being a main character) weren't Chosen Ones. And it turns out that Hollyleaf wasn't one, either.
At the end of Dan Abnett's Gaunt's Ghosts novel Ghostmaker, with the eldar who could have closed the Way dead, Inquisitor Lilith must take his place. The eldar there are struck by her name, which they take as Lileath, and Gaunt points out that her whole life has led there. It merely states, however, that "perhaps" she had been born to do that.
In James Swallow's Warhammer 40000Deus Encarmine, when Arkio picks up the Spear of Telesto, he briefly takes on the appearance of the primarch Sanguinius, and all the Blood Angels (even his brother Rafen) regard the miracle as evidence of his status. Shortly thereafter, one of them observes that those who object to this are dying and those who accept are living, which must be an omen, which is the point at which Arkio says he doesn't want it. But he is talked into carrying on, with all his doubts.
In Deus Sanguinius, both Arkio and Rafen foresee a Cain and Abel confrontation between them. When Arkio's forces confront those under Mephiston, Combat by Champion is proposed. When Mephiston is about to face him, Rafen shouts from among Arkio's men that he will do it. Mephiston reads his mind and discovers that he is not only pure but has been touched by a vision, and he stands aside to let Rafen take the challenge.
One of the Young Wizards novels puts a strange twist on this trope: only at the very end of the novel, right after the Big Bad has been defeated, do the viewpoint characters learn that one of them had always been The Chosen One for that particular battle, and was the only person throughout all the timelines of all the universes who could have possibly pulled it off.
Dune- the trope is thoroughly deconstructed with Paul Atreides and his son Leto. Played straight with Duncan Idaho in the final book.
Not quite played straight in fact, since he was chosen by the Tleilaxu - and it doesn't quite work out as planned.
In The Keys To The Kingdom by Garth Nix, Arthur Penhaligon is designated "Heir to the House" by Mister Monday, because he was supposed to die shortly thereafter, in an attempt to keep the Will at bay. Ironically, this was suggested by the Will itself, and led to Arthur becoming a major threat to the Trustees of the House.
The Black Company decides to protect one after their employer turns on them. In this case she's the reincarnation of The White Rose, a hero who is supposedly able to defeat The Lady. The original was responsible for putting The Lady in the can along with her husband and sorcerers. It's implied that she was able to do this because she nullifies all magic around her.
Dexterity Jones and to some extent Zandakar in Karen Miller's Godspeaker Trilogy. Rhian also displays elements of this trope as she is mentioned by Hettie.
The Giver, anyone? Jonas is chosen by his society to be the new Receiver of Memory, a very revered position. Halfway through the book he decides that pulling a Screw Destiny will work for the better of society in the long run.
In The Restaurant at the End of the Universe, Zaphod Beebelbrox is placed in the Total Perspective Vortex — a machine that tells whoever's inside it exactly how important they are in relation to the universe. This is mainly used as a form of execution, as everyone placed inside it so far has gone insane. However, Zaphod walks (not falls) out triumphant — he really is (as he thinks) the most important person in the universe! Thing is, this gets subverted since he is unknowingly actually in a parallel universe created specifically for the purpose of him surviving the Total Perspective Vortex — thus since the universe was created just for him, he is by default the most important person in it. He then pulls a spaceship out of his pocket and travels through time.
Tamora Pierce's Tortall series has several Chosen Ones, but in each case it's pretty clear who chose them and why. In fact, one girl is chosen by the Trickster God, who poses as the god of war in order to tell some people that she's been chosen. When they finally find out who really chose her, they kick themselves for not figuring it out sooner, because she was a talented spy instead of a warrior.
Subverted in War and Peace, where Pierre Bezukhov determines based on the gematria of his name that he is meant to save humanity by assassinating the anti-Christ Napoleon. Instead, he is captured for an unrelated act and forced-marched across most of Russia, where he learns the true meaning of his life.
Played with in many, many ways before all is through by the prophecy of the Hero of Ages in Mistborn. The Hero turns out to be Sazed. Vin, the actual main character, is also a Chosen One of sorts, but isn't the Hero and wasn't part of prophecy.
Eragon of the Inheritance Cycle seems to be a Chosen One of sorts. Though he wasn't actually named in prophecy, he was chosen by the dragon Saphira to be her rider during the war between the Varden and the Empire. Since he is the only Dragon Rider not on the side of the Empire, the factions aligned with the Varden often laud him as their "only hope" to defeat Galbatorix, as they will fail without him. Not that they're very happy about this, given that he tends to ignore orders, lacks common sense, and tried to seduce one of their leadership figures. The dwarves are implied to conceal deep grudges against him. Eragon himself doesn't much like his position either.
Morgon of The Riddle Master Trilogy can't seem to get a break. The man just wants to farm, but no. Rather he agrees to take a simple journey to answer a dark Riddle (i.e. a prophecy) about the stars on his forehead, which ends up sending him halfway across the continent a few times, and getting him attacked by mysterious shape-shifters.
The Prophecy Of The Stones names four significant people who will play a part in freeing the land. Three of them are girls with specific tasks, who end up getting kicked out of their homes because of the prophecy and questing around the land to figure out what the prophecy means. The fourth is actually called The Chosen One and is tasked with leading the forces of good in the final battle.
Percy Jackson and the Olympians includes a prophecy that says there will be a chosen one that will decide the fate of the gods. No pressure. There is one catch, however. They don't know who it is. All they know is that it is the next child of The Big Three (Zeus, Poseidon or Hades) that turns 16. Eventually it showed that Percy Jackson was the chosen one.
Another, more tragic example, is Luke Castallen, who was always fated to betray the gods and serve Kronos, and to finally perform a Heroic Sacrifice to destroy Kronos.
One Rose Trilogy's Kallista Varyl makes the mistake of offering the One anything she wants if she'll save a city under attack. Turns out, the One wants Kallista to take care of a few things...
In Animorphs, four of the six main characters are chosen by the Ellimist, at least according to the Crayak. (Jake and Rachel were the odd ones out)
Even among those chosen four, however, Tobias stands out. The Ellimist goes to great lengths to ensure his birth, manipulating Elfangor's life in such a way that he would sire Tobias and then be separated from him. He then targets Tobias specifically to save a pair of Hork-Bajir, telling him he is 'a point on which a timeline may turn'. Strangely, the Ellimist's high prediction never seems to go anywhere: while Tobias succeeds in saving the Hork-Bajir, his role in the rest of the series is minimal and ultimately he even opposes the strategy which ends up winning the war.
Subverted in the third Matthew Swift book, The Neon Court. The Neon Court and the Tribe spend most of the book preparing to go to war over a prophesied Chosen One who's supposed to give victory to whichever side she chooses. Except the prophecy was a lie. The two groups are being set up by a third party to go to war and wipe each other out, along with the poor girl who was singled out as the supposed Chosen One.
The true name of Alfred Montbank is the Death Gate Cycle is Coren, which is the Sartan word for "Chosen" or "To Choose". It's apparently a very common name among Sartan, as parents hope their child will be chosen for some great destiny. Alfred comes to hate his name when sheer chance results in him being chosen to be the only survivor of the Sartan community on Arianus.
In The Stand, Mother Abigail is the one chosen by God to lead the side of good in Boulder.
Coryn, in Guardians Of Gahoole fits this. So do Soren and probably Hoole himself. At the time of Hoole's death, the Ember was hidden, and it was fortold a barn owl would come to be the next to retrieve the ember. This was Coryn. But it was also said there would be "another king, un-embered, but Glaux blessed". This is Soren.
Jaenelle Angelline from the Black Jewels Trilogy is Witch, a being born from the dreams of the people of her and other worlds to the end the corruption of two powerful witches. As such, she has god-like powers which surpass all others
Sasha Hunter in Greek Ninja is chosen by fate to protect the world from the evil powers approaching it due to her being the reincarnation of Eli. Also Daichi, who is the Legacy of Hiroyuki and according to the prophecy from Pythia, the task Sasha is trying to carry out cannot be accomplished without him.
Dagger-Star by Elizabeth Vaughan had a prophecy that only a person with a dagger-shaped birthmark can free the land of Palins from its tyrant and become its rightful ruler. It turns out that a lot of people have this birthmark, but most of them are mere children, and the tyrant, thinking that the prophecy only referred to one person, captured a woman with this birthmark and made her a Sex Slave until her mind broke. The Action Girl Red Gloves, not really caring about the prophecy, defeats the tyrant (being a Nay Theist, Red Gloves says that she won because she was a better fighter, not because of some prophecy), then retires and lets another girl with the birthmark named Gloriana become the Queen.
When Rook is in jail at the beginning of In a Beginning he remembers being called to be a Chosen One. As the series progresses, there are hints that it did not go well for him. Especially since after that he was chained to a wall for five years fighting a never ending battle.
Lampshaded and subverted thoroughly with Shan's story in The Chronicles of Magravandias. Shan was actually Taropat's back-up choice since the real chosen one was killed by the Magravandians. Taropat decided to Screw Destiny and create a new hero to defeat Magravandias. Further taken apart by Shan ultimately not being the hero of the story anyway, even if he plays a key role; he is the Warrior, not the King.
In Wrong Time For Dragons by Sergey Lukyanenko and Nick Perumov, the protagonist is an everyman from our world who ends up in a fantasy setting in the "middle" world (between our non-magical world and a world where magic is everywhere) prophecied to be the next Dragon Slayer and protect the "middle" world from another invasion by the Dragons of the magic world. However, he faces opposition from those who wish to see the Dragons win. In a twist, one of the people opposing him is the previous Dragon Slayer, who stopped the previous invasion by killing the lead Dragon, raping his mate and banishing her to the non-magic world. She ended up being the protagonist's grandmother, meaning he's the grandson of a Dragon and a Dragon Slayer.
In the Watch books by Sergey Lukyanenko, Anton and Svetlana's daughter is supposed to be the next messiah, although the ending of the second book makes it unclear as to whether she will be the actual messiah or simply an extremely-powerful Other. As of the sixth novel, we're still not sure, although it's claimed that she has the power to destroy Twilight itself by killing the Tiger, its manifestation, eliminating magic from the world.
Live Action TV
In Charmed, the sisters are referred to as the Chosen Ones. Wyatt Halliwell, Piper's firstborn son, is also known as the Chosen One, and is worthy of wielding Excalibur.
An early episode had a young boy who was the only being who could wield an evil witch's wand for the side of good, as well as kill her.
Not only is Amy Pond the one to, as The Silence so eloquently put it, "Bring the silence," but she is the most important being in the universe, even more so than the Doctor and his previous new series companions.
The title character of Buffy the Vampire Slayer, at least until the end of season one where it becomes subverted when Buffy was drowned and quickly resuscitated. She was replaced by Kendra Young, then Faith Lehane, but for all intents and purposes Buffy was still the Slayer. All Slayers before Buffy (Nikki Wood, the First Slayer, etc) played this trope straight. They rarely live to see their 20s, and tend to be chosen when they're extremely young, at 15-17 if they're exceptionally lucky, and didn't get discovered by the Watcher's Council particularly quickly (as appears to be the case with both Buffy and Faith and many of the Potential Slayers during season 7, but not the case with Kendra, who got an even shorter end of the stick, abandoned by her parents and raised by her Watcher). The "One" part of the Chosen One is very literal - "One girl in all the world." (At least until the end of Season One)
It is indicated towards the end of the series that the replacement slayers are already lined up to take over when their predecessor dies, in significant numbers too. Apparently some get activated a little too early, maybe the Prophecy is incapable of distinguishing when a Slayer is going to be Back from the Dead. In the end of the series, the Good Guys do some magic to speed along the "Choosing" of the potential Slayers, essentially creating an army of girls with their Slayer activated.
The Anointed One was also an intended chosen one, but instead was killed by a vampire who may not have been destined, but also wasn't stuck in the body of a child.
Funnily enough, despite being the one to stand alone against the forces of darkness, there are plenty of characters out there who make the Slayer look pathetic in comparison. Doesn't even have to be a villain, considering Willow is obviously so much more powerful than Buffy in the end. More often than not, Buffy has to rely on her team's help or some quick thinking to defeat any given villain. Like using an anti-tank rocket launcher (stolen by Xander) to take out The Judge, a demon who could kill her by touching her.
In The Nine Lives Of Chloe King, the title character was a prophesied 'Chosen One' destined to unite the prides of the cat beings called the Mai, of which she is one.
Locke on LOST appears to have been chosen for a special role. We just don't know what the role is or by whom he was chosen. Ben apparently used to be the chosen one. As he tells Locke, "Destiny is a fickle bitch."
In an incredibly cruel twist, it seems his special role, his destiny was to die off Island and return so that Jacob's currently unnamed rival could pose as him and kill Jacob...and despite being said to be chosen by Jacob, he never even met the real Jacob while alive, implying that maybe the whole "chosen one" thing was just crap thought up by Jacob's nemesis (whose current Fan Nickname is Esau) so that he could return to life.
It now turns out that he was already one of a number of people selected by Jacob as candidates to succeed him. Other candidates include Jack, Hurley, Sayid, Sawyer, and "Kwon" (either Sun or Jin).
In Carnivàle both Ben Hawkins and Brother Justin are chosen ones on opposing sides, following in a long line of both good and evil avatars. Also, Sophie is revealed to be the final avatar late in the series.
Clark Kent in Smallville is referred to as a sort of 'chosen one' by the local indian tribe, who call him 'Naman', the prophesied warrior who would destroy his worst enemy, Sagith. In fact this prophecy was implanted in the tribe (along with metahuman werewolf powers) by a Kryptonian visitor centuries ago.
Fast forward about 13 years, and we have the prophecy of The Light: a person born from the most powerful sorceress and the most skilled swordsman who is destined to defeat the forces of darkness. Power Rangers Mystic Force played this trope completely straight.
In Babylon 5 there is not just 'One' Chosen One but three of them! Or, alternately (and significantly), one One with three parts (as Zathras puts it, The-One-Who-Was, The-One-Who-Is, and The-One-Who-Will-Be).
Retcon doesn't even begin to describe B5. JM Straczynski practically deserves to be listed under the Crazy-Prepared trope for his contingency planning. From the very beginning, every single major character, in all five seasons had an "out" written into the story so that they could be removed without affecting the storyline, and indeed, could be reintroduced later if necessary.
And he specifically stated in interviews that it was intentional to remove Sinclair (a popular character on B5) during the height of the series. Straczynski designed the show to have a beginning, a middle, and an end (plus 20,000 contingency plans) unlike most shows. But Sinclair leaving and coming back in later seasons was not a contingency plan - it was JMS's decision (he realized that Sinclair's Character Arc had played out too quickly, so he had Sinclair Put on a Bus until he was needed again).
The trope is also subverted heavily in "Comes the Inquisitor." During this episode, the Inquisitor (on behalf of the Vorlons) tortures Delenn and Sheridan until they both proclaim that they're nothing special, that if they're killed others will just take their places, and that they most likely will die pointlessly and without glory.
That is revealed to be true. Sheridan ascends and leaves beyond the Rim, while Delenn dies of old age.
Dr. Gaius Baltar is 'chosen' by the hallucinatory vision of the Cylon Number Six to serve the One True God, and she manipulates him to that end over the course of the entire run of the series, from scientist to political leader to champion of the downtrodden underclass to religious icon. She actually calls him 'the chosen one' on several occasions. Interestingly, no matter what happens, the things Baltar must do as the chosen one also get him laid.
In the second instance, President Laura Roslin comes to believe that she is the dying leader who will lead the people to Earth, based on her interpretation of ancient religious texts. Her role is questioned when she is cured of her supposedly terminal cancer, and reassessed when she suffers a relapse.
The third possibility is Kara 'Starbuck' Thrace, who is told early on by the Cylon Leoben that she is important and has a destiny. Unlike the other two, she actively denies it and works against it, before embracing it shortly before her 'death' in the atmosphere of a gas giant. Upon her return, she comes to passionately believe she is now the one destined to lead the human race to Earth, unaware of a Cylon prophecy that she will actually lead the human race to the apocalypse.
The fourth example (is that a record?) is the Cylon Number Three (D'Anna Biers), who becomes obsessed with seeing the faces of the Final Five and what lies between life and death. She declares herself to be a chosen one who will lead the Cylons into a new age, but instead her hubris kills her and leads to her entire line being boxed. It turns out her experiences were actually more important to furthering Baltar and arguably Starbuck's positions as 'chosen ones' (by putting Baltar in a position where he found his way back to the fleet, and by enabling Starbuck to find Earth).
Captain Dylan Hunt on Andromeda started out as a normal human (albeit genetically upgraded, which is standard for 90% of human characters in that series), but as seasons wore on he was retconned to be a half-human/half-Sufficiently Advanced Alien of the Master Race, then became the Paradine, spoken of in ancient prophecy, with his own prescient alien seeress by his side. (Trance Gemini, who started out as an (seemingly) innocent perky alien girl with hints of unusual powers, but in later seasons was transformed into a God Mode Sue.) Hercules in Space, indeed.
Sam Winchester of Supernatural. Sam is essentially the chosen one of the series. He was chosen to be the vessel for Lucifer. Everything that has happened, including the death of his mother, to Azazel/YED bleeding in his mouth, to the development of Sam'a special abilities has led up to the fact that Sam was the one that would eventually destroy the world.
Dean Winchester as of Supernatural season 4. Unfortunately, the guy's gone through so much Break the Cutie trauma by this point, that it's doubtful if he can actually fulfill this role. In season 5 it's revealed that he's the intended vessel of the Archangel Michael, which he doesn't agree to.
He's also a Seeker. There were others before him, whenever situation was grave enough to warrant one. Each one is implied to have had his own Confessor and a wizard (at least the one before did). Unfortunately, the one before ended up sleeping with his Confessor and going mad after the wizard convinced her to commit suicide. The wizard ended up killing the Seeker with the Sword of Truth and putting an enchantment on his body to keep his spirit out of the underworld. He then hid the truth (claiming that both the Seeker and the Confessor died in the final battle against the enemy) in order to keep the people's faith in the Seeker.
In the series of books the series is (very) loosely based on, Sword of Truth, it is suggested with hints spread out over the different books that the titular sword was actually made for the main character and the whole line of seekers was a tool just to get the function and authority to him.
A Bit of Fry and Laurie parodies this in the first sketch of season 3, which features a father telling his son that he's the Chosen One just to get him out of the house.
The Collector: Morgan was God's chosen instrument to discover the cure for Plague, centuries ahead of reality. The Devil successfully distracted him from this role.
One episode involves a great spirit periodically guided to an Amerindian tribe, the latest being their needed savior, whom the Devil also tries to distract from her role.
In Once Upon a Time, Emma Swan, the daughter of Snow White and Prince Charming is prophesied to one day save all of the fairy tale characters trapped by the Evil Queen's curse which has them living out mundane lives in our world with no memory of who they really are, and no chance to reclaim their happy endings on their own. Played with in that the only one in-universe who actually believes this is Henry, Emma's son (at least, on the surface).
Oddly enough for the idea, is that Emma fulfills her destiny at the end of season 1, but still has a ton of work to do protecting the town now.
The title character of Merlin, who was chosen, we haven't a clue by who exactly, to help Arthur become the king he is destined to be and help him unify Albion.
Actually, it's Arthur who's the Chosen One. He's just such a Chosen One that fate gave him his own Chosen One to keep him alive and sane throughout being a Chosen One. His wife Guinevere is a Chosen One too, with a destiny so sure that the most powerful healing artifact in the Five Kingdoms could not stop a dream of her becoming queen, because fate had decreed it. In other words, he's such a powerful Chosen One that all the people in his life become Chosen Ones just by being around him.
Duncan MacLeod in Highlander: The Series. First there's Cassandra's prophecy (not the mythological Cassandra) about a "Highland child born on the winter solstice, who has seen both darkness and light and who will defeat the voice of death" and then there's the whole Ahriman/immortal champion thing. A few fans think that might be what the prophecy meant, rather than referring to Kantos, but it was all still really bad anyway.
Vlad Dracula from Young Dracula is the Chosen One, prophesised to bring the vampires out of hiding.
In Being Human, Eve, the newborn daughter of George and Nina, is the Chosen One, who is going to save the world from the vampires.
In Star Trek: Deep Space Nine, Captain Sisko is the Emissary to the Prophets, the Wormhole entities that the Bajorans worship as gods. It takes a little while for the science-loving Sisko to embrace his role as the messiah of another race, but he manages. Sisko later learns that he is actually a Prophet's son (his mother briefly took on human form to give birth to him before leaving him with his human father). Over the course of the series Sisko, in his dual roles as Starfleet officer and Bajoran Emissary, saves Bajor from military and spiritual threats.
Despite him never being called this, Hiro of Heroes kind of becomes this when his destiny is to Save The World and "kill" Sylar.
Troy Barnes in Community, who's destiny is to be....the greatest air conditioner repair-man ever. Yes, its apparently Serious Business, for the One True Repair-Man Will Repair Man.
Nina Martin in House Of Anubis. Joy Mercer might also count, as she is not the chosen one, but was believed to be. Sarah Frobisher-Smythe, too, as she was the chosen one before Nina was born.
Both Jeff Jarrett in WCW and Drew McIntyre in WWE have been specifically referred to as "The Chosen One." In both cases the divine destiny was more the fact that they were well liked by the bookers, with Jeff being personal friends with Vince Russo and Drew apparently being a favorite of WWE owner Vince Mc Mahon. Jeff has had some ups and downs with his chosen one gimmick. Drew was, at first, nearly universally reviled by the internet wrestling community as most found him to be very boring in the ring and on the mic. However, after he lost the Intercontinental Championship and was stopped being pushed as hard, Drew became an Ensemble Darkhorse.
Played with in the BBC Radio 4 play ElvenQuest, in which the Chosen One is the protagonist's dog.
Jesus Christ means "Jesus the Annointed One". Christos being Greek for "anointed" (and "chrism" is an old name for the anointing oil). Thus "Christ" is a title, not a given name.
The fourteenth Dalai Lama, as well as his predecessors, were all chosen because they were believed to be the reincarnations of the boddhisatva Avalokiteśvara. Supposedly the current Dalai Lama was shown a bunch of household items at the age of two, some that belonged to the previous Dalai Lama and some that didn't. He was then asked to determine which of the objects were his. He got every one right.
In Exalted, you're a Chosen One-in-three hundred/one hundred/fifty, depending upon what Exalt you chose.
If the Alchemicals were to unite, they would be a Chosen Army.
Dungeons & Dragons 3.5 Edition has the Favored Soul class, a character with an intuitive connection to a deity who can spontaneously cast divine spells. They are also automatically proficient with their deity's favored weapon, and gain bonuses to using it as they level up (traditional Clerics, on the other hand, may be able to summon self-wielding versions, but aren't proficient by default). They are also one of only two base classes in the game that has no weak saving throws.
Suikoden - every major game in the series revolves around the 108 Stars of Destiny, 108 usually recruitable characters that all play a vital role in the fate of reality.
Xenogears revolves around a Chosen One named Fei who is a reincarnation of the original Chosen One, Abel. His choosing is eventually revealed to be sheer accident, as his contact with the Wave Existence occurred because Abel got lost while trying to escape the doomed Eldridge. His contact allows him to survive and entrusts him with the task of freeing the Wave Existence from the Zohar, and he is destined to die and be reborn forever until he accomplishes his task. Ironically, if Abel had not gotten lost, someone (or perhaps no one) else would have become Chosen One.
The game has another Chosen One, Elhaym. The Wave Existence created the original Elhaym out of Abel's longing for his mother (he was lost, remember?) and she likewise reincarnates across several lifetimes.
A number of Dragon Quest games have a Chosen One, though the method of choosing differs. In DQ1, the hero is chosen by virtue of being the descendant of a great hero. In DQ2, er, ditto. In DQ3, the same thing happens, but the hero goes on to become the great hero of legend referenced in DQ1 and 2. DQ4...yeah. DQ5, the protagonist is actually not the Chosen One, but his inevitable son is.
Colette Brunel from Tales Of Symphonia, although she's not the main character and has been fully aware of her status as the chosen one her whole life, it being due to her genetics. This is also a deconstruction. It is revealed that there are entire families containing the chosen bloodline spread across the world, any member of whom can be proclaimed the chosen one by the Powers That Be whenever required. And then there's the whole issue of what it turns out that the chosen is really chosen for...
Zelos Wilder is another chosen (the chosen of a different world, to be precise), but he doesn't really want to do it — in fact, at one point he either pretends to or actually does make a deal with the villains to betray the party in exchange for getting out of his duties.
In Tales Of Eternia, it's implied that Reid and Ras were Chosen ones; but not entirely any specific one as more "Only these people can use the power of Seyfert's Fibril". Meredy can too, thanks to Shizel, user of Nereid's fibril being her mother and all.
The 2004 The Bard's Tale parodies this rather savagely. You are told early on that your character is the chosen one on an important quest, but as you progress through the game, you encounter a number of self-proclaimed Chosen Ones who make big speeches about their destiny, only to get killed horribly by monsters or booby traps. You eventually stumble across a whole prison full of "Chosen Ones" of various ages.
The best part being the creepy goblins that show up and sing a song about the latest Chosen One to get its ass kicked. Little bastards.
It's bad luck to be you, A chosen one of many isn't new...
The Reveal that Caleigh the princess is actually the demonic Big Bad of the game actually makes the situation pretty tragic. A demon has been tricking countless poor saps into getting themselves killed, trying to find someone skilled enough and gullible enough to free her.
In Fire Emblem: Radiant Dawn, the characters that enter the game's final tower are classified as "Chosen Ones". The player gets to choose most of them though, rather than fate directly.
Notable aversion in Grandia: The protagonist Justin is an ordinary boy who just wants to be an adventurer. He isn't chosen by the "Spirits" after an ancient prophecy, but is begrudgingly accepted by them after proving how awesome he is.
Link from Zelda; in some of the games he's specifically referred to as "the Chosen Hero."
Interestingly enough, in later games, Link actually has to earn the title of Chosen Hero. Most notably in The Legend of Zelda: The Wind Waker, where simply being on a quest to defeat the Big Bad isn't enough, he also has to recover the pieces of the Triforce of Courage and show that he's courageous enough to actually receive it in his various adventures. His was probably because the out-of-timeline-erasure of the last Chosen One caused the Triforce to burst into 8 powerless fragments, which could not seek a bearer for themselves, like a complete Triforce-piece does. It still probably had to be Link and nobody else, since the Triforce probably wouldn't have accept anybody else for a "host".
That's not just the later games. Proving his destined right to find and wield the Triforce of Courage is the entire point of Zelda II The Adventure Of Link. That's when the existence of the Triforce of Courage is first mentioned; the original game had only Wisdom and Power.
Zelda (the Zeldas?), too, would count as a Chosen One; seeing as how she received the Triforce of Wisdom. Ganondorf, though, he has the Triforce of Power, not so much; he unconsciously chose that one himself. The Zelda of The Legend of Zelda: Skyward Sword is specifically referred to by Fi as one of great destiny and purpose, which officially deems her as such in-universe. Although it's later reveal that Zelda is Goddess Hylia mortal reincarnation, so she isn't The Chosen One as much as God in Human Form.
The Keyblades in Kingdom Hearts tend to choose keybearers for themselves when needed. This part goes to Sora and later also to Mickey Mouse, Riku, and Kairi. Once chosen, a keybearer has to deal with a great amount of Heartless and Nobodies, who want to kill him/her because keyblades are the only true threat to them and also simply Because Destiny Says So. Additionally, Sora was also chosen to open "the door to light" with his keyblade for reasons as yet unknown.
Interestingly, Sora was never meant to wield a Keyblade. The one initially chosen is actually Riku, but since Riku jumps too quickly at the call, Sora finds it instead. Terra chose Riku, but destiny chose Sora. They're both Chosen, but Destiny's Choice takes precedence. Meanwhile, Aqua planned on choosing Sora, but decided against it after realizing that Terra had chosen Riku...unaware that she had already chosen Kairi by accident.
Although ultimately subverted It's revealed in Birth By Sleep that at one time in the past hundreds to thousands of people wielded keyblades, and that a massive war erupted between them. The keyblade wielders of the present are few just because there were few left over after the keyblade war to pass on the ability.
In the online Flash RPG, Adventure Quest, You are the Avatar of Hope, though it has been implied that the entire human race of Lore is the Avatar of Hope, in one of the stories posted by the admin Falerin on the forum.
Your character in The Elder Scrolls III Morrowind is generally assumed to be a Chosen One thanks to the prophecies of the "Nerevarine," the reincarnation of the heroic Nerevar Indoril. This trope gets subverted a ways into the storyline, when your self-appointed mentor explains that "having the spirit of Nerevar" isn't literal...you're not the reincarnation, you're just qualified to follow in his footsteps and save his people from his ancient foe. In fact, there are others qualified to become the Nerevarine as well, and you'll even meet up with a few who tried and failed. So really, you don't save the day Because Destiny Says So, but because you say so.
They take their Chosen Ones seriously on Vvardenfell, really. One of the Tribunal Temple's standing orders is to execute anyone calling themselves Nerevarine...not because they want to stop the prophecy but rather because if the Nerevarine is going to fulfill every point on his prophetic agenda (yes, there's an actual list) he can't let a little thing like a full inquisitorial execution stop him. Ergo, try to execute every pretender - if they succeed, they know it was an imposter.
It is also implied that it may all be a set-up by Azura to get revenge on the Tribunal for going against her when they obtained their godhood. The Emperor is speculated by at least one NPC to be setting you up as the Nerevarine for PR (though the 4th game establishes The Emperor is a strong believer in prophecy).
It is further implied that having the spirit of Nerevar will become more literal as you follow in his footsteps (Elder Scrolls metaphysics allows for avatarizing yourself by 'walking like he does until he walks like you do').
In The Elder Scrolls IV Oblivion, the player character is a Chosen One who is supposed to take the Emperor's mystical MacGuffin to the his surviving son, another Chosen One. Sometimes it seems the gods spend their time just choosing people to do stuff. It is a world guided by prophecy...
The player character can also be a villainous Chosen One, in which he or she meets the goddess who did the choosing while you "were in the womb", if they complete the "Dark Brotherhood" quest. All while still being a heroic Chosen One in the main quest.
The Elder Scrolls II Daggerfall, meanwhile, notably averts this; the main character is only sent on the game's (main) quest because they happen to be a friend of the Emperor, who needs it done discreetly.
Played with in The Elder Scrolls V Skyrim. The Dragonborn is one of those rare individuals in the setting who are not bound in any way by fate, beyond being gifted with the soul of a dragon and thus being able to use the Thu'um. However, those exact two properties are why every metaphysical force in the setting wants the Dragonborn on their side.
The first property applies to every player character in the series. They may or may not be bound by the relevant prophecy (and they by definition are controlled by external forces), but they are free from ordinary fate.
Played very straight in the Dark Brotherhood and Mage's Collage questline, where the player is declared the chosen one of the Night Mother and Psijic Order respectively, in both cases very early on. Amusingly, even earlier you can choose to wipe the Dark Brotherhood out instead.
Metroid: Samus is sometimes portrayed simply as a singularly hyper-competent one-woman space police force, but in the NTSC version of Metroid Prime, the Chozo Lore entries imply that the Tallon IV Chozo prophesied and expected Samus to come save their dying planet after the Phazon meteorite strike.
Valis: Yuko Ahso is generically thrust into the spotlight as the warrior who can wield the sword of Valis and defeat evil. (Okay, not quite generically—she's thrust into the spotlight with a big dose of Fanservice and Stripperificness. She plays the role of The Valis Warrior in the first three games, then becomes the Dream World's goddess, and in the fourth game, Lena takes over Yuko's prior role as the wielder of the eponymous legendary sword.
Unreal has various messages (combined with your actions) that heavily suggest that you are The Messiah who will save the Nali from the tyranny of the Skaarj. This may be a subversion however, as the tournament games (said to be set after the first game) suggest that the Nali are still being hunted, although the reference is non-specific enough that you could easily assume your character at least made their situation far better.
Fallout 2, wherein the player character is identified as the Chosen One at the very beginning. Apparently being descended from the hero of the first game includes inheriting some pretty big expectations.
The player can also declare himself to be the Chosen One to many characters throughout the game world. Most of them will then treat your character as delusional, insane, or just as a plain backwards tribal following the statement.
Subverted in Arcanum Of Steamworks And Magick Obscura, where it appears that the player character is the reincarnation of the Living One, a mystical figure, but later in the game You discover that you are just a common person, that the prophecy of the reincarnation is false, and that the Living One is in fact still alive.
The prophecy is still subverted in other ways, such as the 'great evil' of ages past — that is, the 'evil' version of The Chosen One you've been sent to smite — being the almost completely helpless prisoner of the realBig Bad. And he's actually a pretty decent guy who, in his centuries of confinement, has had a chance to mull over his past actions and decide he was in the wrong.
Divine Divinity has you being one of the chosen three, the Marked One, one will then be selected by the Council of Seven to serve as Divine One. You become Divine One after the enemies kill other two Marked Ones.
The Legacy of Kain series plays around with this, not getting around to deciding just who's The Chosen One, or what they're chosen for, until the end of the series. In Defiance, both Raziel and Kain believe they're the Champion of the vampires. Eventually, it's revealed that Raziel could be the Champion of either the Vampires or the Hylden, and as the only one with free will, he can choose. In the end, Raziel plays out both Champions' parts by giving the Hylden Overlord a sufficiently strong host body in the form of Janos Audron, and giving Kain, the Scion of Balance, everything he needs to fulfill his own destiny by erasing Nupraptor's corruption from his spirit and fusing himself with the Soul Reaver.
Secret of Mana also plays with this trope. Near the start of the game, the main character pulls a sword out of a stone. He is later told that only a great hero should be able to remove the sword, but since he is too young to be a hero, it must have happened because the power of Mana is weakening. He is asked to take care of the sword until he can find a real hero to give it to. Later on it turns out that he was The Chosen One all along. He's even the son of a hero!
The sequel, Seiken Densetsu 3, also handles this trope in an interesting way since there are six characters to choose from, and you can choose any one of them to be the main character. Destiny doesn't choose The Chosen One until shortly into the game when your first character finds a weakened fairy looking for somebody to save the Mana Tree. While you inevitably fail to save the Mana Tree, your fairy friend becomes the new Mana Goddess who will eventually be able to restore it.
In Famous: Played straight. If you collect enough dead drops you eventually come across one of a phone call made by Kessler to the courier service Cole worked for. He asks for Cole by name to deliver a package, which is how Cole gets the Ray Sphere in the first place when he is instructed to open it. Might be an aversion given that technically he chose himself given that Kessler is Cole from the future.
The Player Character in the Baldur's Gate series gets some of this in Throne of Bhaal. It turns out the outcome of the prophecy of the Bhaalspawn hinges upon them; the great destruction foretold will only happen if they fail.
Prophetic stone head:
"The wheels of prophecy e'er turn,
Gorion's ward hath come.
Crossroad of past, present and future,
The one foreseen, the one foretold."
BioWare has actually been moving away from this lately, the player characters in both Mass Effect and Dragon Age are not so much the Chosen One prophesied to save the world as the only one who can save the world through a combination of circumstance and badassitude.
For Mass Effect, one character proposes in Mass Effect 3 that Shepard is the Avatar of his/her Cycle, someone who plays a centrally important role in the fate of the galaxy. Shepard even has the opportunity to recruit the Avatar of the previous cycle, Javik. With the Extended Cut, it is possible for the game to play out such that Shepard fails to stop the Reapers, but Liara succeeds in warning the next cycle, allowing them to stop the Reapers 50,000 years later. Shepard becomes Shrouded in Myth for his/her part in this.
They have actually subverted it completely in Dragon Age II; everyone assumes that Hawke, the Player Character, deliberately caused the momentous events that occurred in the game, while really s/he was just in the wrong place at the wrong time, had absolutely nothing to do with everything that was going on, and was forced to use badassitude to ride the wave. In fact, it can be argued that in the end, Hawke really changed nothing.
Arc The Lad subverts this tropes: Arc was not chosen by the Powers That Be: he was chosen by his father who then went to bargain with the power that be.
In Super Paper Mario, it's stated that Mario, Luigi, Peach and Bowser are the Heroes of Light chosen by the Light Prognosticus. Luigi is the Chosen One for the Dark Prognosticus, being the Apocalypse Maiden.
Yoshis Island DS has the Star Children: Mario, Luigi, Peach, Wario, DK, Bowser and a newborn Yoshi (Implied to be the Yoshi from when Mario is an adult).
EarthBound had the Chosen Four. With Ness as a more specific Chosen One.
Final Fantasy X was a deconstruction. Chosen One? You're going to die in vain, and if you do the thing you were chosen for, the Big Bad keeps living.
Final Fantasy XIII has the l'Cie. They are chosen to complete a mission assigned by a fal'Cie, a mission which's nature is completely unknown to the l'Cie in question. They are distinguished by a mark on any part of their body, such as this one.◊ If a l'Cie fails to carry out its quest, s/he get turned into a Cie'th, Body Horror incarnate, as punishment; and if the l'Cie succeed his/her quest s/he will turn into crystal until the fal'Cie decideds to give the l'Cie a new mission to carry out... It kind of sucks to be a Chosen One in Final Fantasy XIII's universe.
Trilby, and to a similar extent, Theo Decabe, are referenced to being chosen ones in the Chzo Mythos. Trilby is "The Guide" and Theo is chosen to be "The New Prince"
The protagonist of Ogre Battle: March of the Black Queen is decreed by Warren the Seer to be the hero who will liberate Zenobia. If you choose to have the protagonist fight against Rashidi, he mentions how he foresaw the protagonist's coming and his death at the protagonist's hands.
Hoopz Barkley of Barkley, Shut Up and Jam: Gaiden: Chapter 1 of the Hoopz Barkley Saga. Whatever he's chosen for, it has absolutely nothing to do with the game itself.
Eternal Darkness deconstructs the concept of the Chosen One in that it demonstrates that it's probably a very good idea to figure out who is doing the choosing and to what end.
Septerra Core. The appropriately-named Chosen think that being the descendants of Marduk's army make them this collectively, and Doskias in particular thinks that being Marduk's direct descendant (which means he's the great-great-great-great-etc. grandson of God) makes him The Messiah as well.
Tidus in Final Fantasy X. He was brought to Spira by Jecht who, upon becoming Sin, decided that Tidus should be the one to defeat him.
The Assassin's Creed series has the modern protagonist, Desmond Miles, acting as a conduit for the Genetic Memory of his Assassin ancestors, as part of a scheme by the modern-day incarnation of The Knights Templar to locate ancient artifacts that will let them control men's minds. Well, it turns out that this is itself part of a much older scheme by the makers of said artifacts to create a nexus in time through which they can communicate with Desmond and tell him how to avert The End of the World as We Know It. Thus, Desmond comes from a family of Chosen Ones.
Word Of God states that they made Desmond's ancestors Altair and Ezio come from separate bloodlines because they wanted Desmond to be the culmination of multiple Assassin bloodlines that carry Precursor genetic material. Desmond is the Chosen One because he carries such a high concentration of Precursor DNA.
The Fateless One in Kingdoms Of Amalur Reckoning is normally The Unchosen One because he/she is Immune To Fate. However, it is because of this property (and generally being a Badass) that the godlike Akara in the "Legend of Dead Kel" DLC chooses the Fateless One to carry out his goals. Just because the Fateless One isn't bound by Fate doesn't mean he/she can't still be manipulated in other ways.
Played with in Guild Wars. The White Mantle seeks out people who are deemed to be chosen ones by fate it seems. Given how many, it apparently doesn't take much to be one of the chosen ones it seems. However, It Sucks To Be The The Chosen One as the White Mantle will try to sacrifice you on a bloodstone. This means that the prophecy can't be fulfilled to destroy the Mursaat. It's revealed over the course of "Prophecies" that the player character(s) are Chosen too, but it's also implied that they aren't the chosen one, so much as the only ones of the Chosen who got there.
Weaponlord is an interesting example, as all the playable characters, including the Big Bad are all considered the Chosen One by virtue of being born under a sacred event called the Warrior's Moon.
The World Ends With You also is an interesting example. Neku is just another player of the Reapers' Game, among dozens of other dead guys/gals. Later in the game, it's revealed that Neku IS actually the chosen one... And he was chosen by Shibuya's resident Jerkass God just because he was staring at a graffiti wall.. However, in the Secret Reports Hanekoma reveals that Neku has "dense and all-inclusive Soul" and "high Imagination" and was therefore picked by the Composer for his qualities (that are the reason that Neku can use all sorts of pin while his fellow Players cannot). The graffiti wall in the UG attracts people with those qualities, so Josh just knew that Neku was the right person. Which makes Neku a true Chosen One... Or sort of that.
Parodied in Borderlands 2, where unscrupulous Arms Dealer Marcus Kincaid tells an egotistical nerd that he is the Chosen One of a random prophecy that he made up on the spot (and changes when necessary) for the sole purpose of selling him a gun for two million dollars.
The Jedi Knight player character from The Old Republic. Every plotline leading in to the game from other media ends in his/her campaign, and there is an actual prophesy about them in the prequel novel.
In 8-Bit Theater, Black Mage and Fighter were chosen by their avatars to fight for the fate of the world. Both deities give up.
The Light Warriors themselves are chosen ones, too. Except they spent too long level grinding so the king got tricked into thinking some other idiots/jerks were the light warriors, and in the end four White Mages end up killing the Big Bad anyway
All four of the protagonists in Homestuck, with the titles "Heir of Breath", "Seer of Light", "Knight of Time", and "Witch of Space". It's also been recently shown that the Sburb beta becomes Unwinnable if any of them permanently dies. If they can't win the game, they can't reconstruct the world after it's been destroyed by the war between the Light and Dark kingdoms.
A Magical Roommate: An oracle of Umbria made a prophecy, and everybody immediately assumed it was about Aylia.In a rare subversion, it was about her friend X, who nobody had ever heard about. Go figure!
In The Order of the Stick, Redcloak is the true prophet of the Dark One, destined to make goblinoids a force to be reckoned with in the world. Redcloak's theological revelations are "refreshingly direct":
Dark One: Don't screw this up. No pressure, though.
Although, he was "chosen" for a rather specific reason: there was no one else for the Dark One to pick. He was the newest acolyte to the religious order, but also the only one to survive the Sapphire Guard's massacre of his village.
Subverted in Our Little Adventure. Julie is the third person the Palm Tree Ghost has sent on this mission. If she fails/dies, it's highly likely TPTG will just choose someone else.
In Sarab, the Apprentices are chosen early in life to be the bearers of knowledge in their world.
Subverted in Wizard School: Everyone at Bumblebane's Magical Academy thinks Graham is The Chosen One. He's actually a fake planted by the Big Bad, Wyrmspawn. Everyone dismisses the fact that Graham far older than the Chosen One is supposed to be and ignores the fact that he's a completely awful person.
In The Gamers Alliance, Marcus is destined to become the King of Remon and the wielder of the magic sword Dusk. Ax is considered to be the chosen wielder of Dusk's sister sword Dawn but after Nergal's emotional taunting she begins wondering if she's not actually the intended wielder but only meant to deliver the sword to the true chosen one.
Jonas Wharton in LG 15 The Resistance is described as "the One", because he is the only trait positive male. Maggie also arguably qualifies, with her super-speshul magic blood.
In the Whateley Universe, every few centuries, when The Balance is threatened, the Tao requires a mortal to take up the magical jade sword Destiny's Wave, and become the Handmaid Of The Tao. The Handmaid is always a beautiful teenaged Chinese girl, but Chou Lee, the current Handmaid, was chosen by the Tao, and transformed by the sword from a chubby white boy from Knoxville, Tennessee called Alex Farshine.
In season four of Red vs. Blue, Tucker becomes the chosen one for an alien prophecy after finding a sword (which he kicks ass with). The prophecy included a lot of Great things.
Terra Murphy, a young girl in Engines Of Creation is given the abilities of a Green Seer immediately after her arrival in the Pactlands through birthright.
In Phaeton Trayen is this, but whether he is supposed to save the world or destroy it is unknown so far.
Fry: "So I really am important? How I feel when I'm drunk is correct?" Nibblonian: "Yes. Except the Dave Matthews Band doesn't rock."
Ron Stoppable from Kim Possible is the chosen one with his Mystical Monkey Power, a power than eventually made him the strongest person by far in the entire series. Never mind that the power in question was supposed to just be a one shot thingy...
Subverted in The Adventures of Jimmy Neutron. Sheen Estevez is called "The Chosen One" by the monks of Shangri Llama, thanks to his strange ability to put his foot behind his head. However, he isn't the 'true'' Chosen One, but merely a substitute (since the monks were sick of waiting around for the real one to show up).
Rikochet Buena Girl And The Flea from ¡Mucha Lucha! The Return Of El Malefico. They are The Chosen One because they can stop El Malefico from taking over the world.
The title character of the show Mighty Max was a twelve year old boy who had been chosen by "Destiny" to be the hero of the series. He was equipped with a cosmic cap capable of opening portals that led to all sorts of places around, in, and over Earth, though it couldn't make new portals.
In a Yin Yang Yo episode, Yin and Yang end up in a magic school, and they meet an otter named Terry, who is the Chosen One. He keeps saying this with dramatic fashion. It's a parody of Harry Potter, really.
The Fairly Oddparents: In the Wishology trilogy, Timmy is declared the Chosen One, and he takes every opportunity to remind everyone that he is. He only is because, as it turns out, someone else Missed the Call. Although its shown in Wishology part two that Turbo Thunder lacked the qualities necessary to be the true chosen one when he tries to attack the guardian of the ice wand without provocation. Timmy on the hand chose to ask for the Guardian's help, proving himself to be the true chosen one.
Zak Saturday of The Secret Saturdays is suspected by his parents to have been born to counter the Kur Stone, thus stopping a massive army of killer cryptids and saving the world, if need be. Now that it's been revealed that Zak ''is'' Kur, it's destiny for Zak to take over the world (as far EVERY SINGLE CRYPTID on Earth is concerned).
Jack of Xyber 9 New Dawn is the only one who can defeat Machestro, who is threatening to destroy and take over the kingdom. The show actually takes from King Arthur legend.
In The Simpsons episode "Homer the Great", Homer is revealed as The Chosen One of the Stonecutters, the secret society that controls the world. However, his actions as leader annoy the members so much that they all quit and start the Ancient Mystic Society of No Homers.
Transformers: The Movie makes very literal use of The Chosen One, with Hot Rod discovering he is the successor to the now-dead Optimus Prime, fulfilling the prophesy of one who would "light our darkest hour", and being upgraded by The Matrix into Rodimus Prime in the process. He is referred to as "The Chosen One" several times throughout the third season.
Alternatively, this is what "Elita One" means. The choosing person then would be Alpha Trion, but there doesn't appear to be any purpose to it.
Hot Rod is the one who got Optimus killed by interfering right as Optimus was about to finish off Megatron.
Jaga: "For it was written that he would be born of fire, a king to lead his people to victory, against ancient spirits of evil."
South Park is fond of prophecies and Chosen Ones: Cartman, Butters Stotch, Craig Tucker, Kyle Brovfloski, and Stan Marsh have all been some kind of Chosen One, although in four different events and in different ways.
Butters is stated to be some sort of child of prophecy by Aslan, and goes on to save Imaginationland.
Craig is stated to be a Chosen One by being part of an ancient Incan prophecy about defeating giant guinea-pigs.
Kyle is a blatant Expy of Jesus in one episode, willingly paying off everybody's debts from the recession and taking them on himself. You need to watch the episode to see just how blatant.
Stan became the chosen one to the Scientologists, after they determined that his thetan level was identical to their dead prophet, L. Ron Hubbard. Stan went along with all the perks of being "chosen" right up until he realized Scientology was a massive pyramid scheme.
Subverted with the Mysterion (AKA Kenny) who is trying to find the meaning behind his not-very-pleasant ability (constantly dying and coming back to life the next day with nobody remembering what happened). At a crucial moment, the spirit of an alien appears who seems to be claming that Mysterion is his son sent to Earth. Then it turns out it was Mintberry Crunch, who ends up saving the day.
As revealed in the season four finale of Metalocalypse, the members of Dethklok are the Chosen Ones of an ancient prophecy.