There are two characters. Maybe one is never seen, or is only mentioned in passing, or whose face is never seen, or it's a book and the author ain't much for descriptions. These two never meet, are never in the same scene, and/or never interact with the same characters. Eventually it's revealed that they're actually the same person. Note that, contrary to what the trope name suggests, they do not actually need two aliases (i.e. pseudonyms) for this trope to apply - but either the characters in-universe or the reader/viewer (or both) need to believe them to be separate people, until The Reveal.
This trope also applies to Multiple Personalities, so long as characters/audience are unaware that they physically share the same body. It is possible to use this as Character Development if the character assume(s/d) a new alias unbeknownest to other characters, especially if the previous alias and persona are considered dead or status unknown.
This is often a source of Wild Mass Guessing, with fans trying to argue that two different characters are really the same person, usually with no given reason why this person would have another identity.
Contrast Collective Identity, which is Two Characters, One Alias.
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Anime and Manga
L in Death Note isn't just one of the top 3 detectives in the world, he's all of them under separate aliases.
Also, early in the series the audience never sees Light's father around the house, being told that he's working. Turns out it's the police chief that's already been around a few chapters.
Later example: After L's death at his hands, Light assumes control of the Kira Taskforce and presents himself to police around the world under the name "L" while still maintaining his identity as Kira.
Masquerade/Alice in Bakugan. This is a shock even to her.
In Baccano!'s Drugs and the Dominoes, Claire Stanfield not only has the reputation as the world's most violent and dangerous assassin, but is also the greatest challenger to that claim, Felix Walken. Gustavo then makes the mistake of hiring the latter to kill the former (along with his stepbrothers, the Gandors) and violent hilarity ensues.
Also, despite the fact that immortals have magically-enforced difficulty with aliases, Lebreau Fermet Viralesque is usually only known by one part of his real name per identity.
Goji and Abullah in both the original Astro Boy and Naoki Urasawa's retelling Pluto. (In the former, just a disguise; in the latter, an alternate personality.)
Fairy Tail is rather fond of this, with some characters pulling off two aliases via magical projections of themselves:
Councilman Siegrain, initially believed to be the Good Twin of the terrorist Jellal, is later revealed to be Jellal's double created to manipulate the council in a ploy to gather enough magic energy to revive Zeref.
Alexei, a mysterious armored man first seen leading Raven Tail's elite team in the Grand Magic Games, is actually Raven Tail's master Ivan, who places a holographic projection of himself in the rafters while he privately interrogates his son Laxus in person since guild masters are forbidden from taking part in the tournament.
Mato, the pumpkin mask-wearing mascot of the Grand Magic Games, is later revealed to be the King of Fiore himself, Toma E. Fiore. The first indicator of this is when Mato is absent on the second day of the Games, which is the only day the king happens to show up.
In an early issue of Justice League of America Year One, each of the five superheroes makes an acquaintance in their civilian identities - Perez the coast guard stands up for Aquaman in a bar, Lora Denton investigates Hal Jordan's test flight for the FAA, Officer Sherman looks in on Diana Lance's flower shop, Detective Jackson starts working with forensics officer Barry Allen, and supercop John Jones is approached by reporter Cal Redmond and creepy fellow detective Vince Logan. It turns out all of these except the last two are J'onn J'onzz using his shapeshifting to spy on the others. It doesn't go down well.
This is a key point in American Born Chinese. Jin Wang and Danny are the same person, even though their stories are told in parallel. The aliases are used to emphasize the (cultural) differences in the character as he struggles to define his identity.
In-universe, every superhero with a secret identity.
This was the original plan for the X-Men character Xorn by creator Grant Morrison; after a long time serving on the team, Xorn unmasked and turned out to be Magneto. Ultimately subverted by Executive Meddling when Xorn was retconned as an original character who believed himself to be Magneto.
In Scott Pilgrim vs. The World, there are several references to Scott's band wanting to attract the attention of G-man, an influential producer. Ramona also makes some off-hand references to her previous boyfriend Gideon. These two both refer to Gideon Graves, who is the Big Bad.
Also the fact that Scott and Ramona are talking about the same Todd. Oh no, indeed.
In TRON Legacy, Castor, Zuse's gatekeeper, actually is Zuse.
Also inverted and subverted. Clu allows Sam to believe he's Kevin, but by the time he reveals otherwise, Sam's in the process of working it out himself.
Sam pulls this on top of the Encom tower, when he reveals to the security guard that he is Kevin's son, and as such is in charge of the company. Then he jumps.
In Batman Begins, Bruce meets Ducard who acts as a spokesperson for the legendary Ra's al Ghul. It turns out that the Ra's al Ghul that Bruce had met was more likely to be a decoy while Ducard is the actual Ra's al Ghul.
In Wreck-It Ralph, King Candy, the ruler of the Sugar Rush arcade racing game, is revealed in the climax to be Turbo, the hero of an older generation racing game who is notorious amongst his fellow video game characters for hacking a newer game out of jealousy, and now tries the doing the same to Sugar Rush.
Chetter Hummin/Eto Demerzel/R. Daneel Olivaw of the Foundation series.
Preem Palver, farmer/First Speaker of the Foundation. If you know Latin you could figure it out.
For that matter, in the second half of Foundation And EmpireMagnifico Giganticus, who claims to be The Mule's escaped jester is actually The Mule. The fact that nearly every description the reader gets of The Mule comes from Magnifico (it's explicitly pointed out that Magnifico is so clearly terrified of The Mule that his descriptions are probably grossly exaggerated) helps obscure this.
The first Foundation one is also a pun Cheeter Hummin- he's not really human- he's an android.
Scylla/ Henry Levy in Marathon Man. The novel makes a big secret out of it.
In Agatha Christie's Murder on the Orient Express, Mrs. Hubbard is actually Linda Arden, Daisy Armstrong's grandmother. This is, to the best of my recollection, not foreshadowed in any way, except to know that the latter is an extremely gifted actress.
Another Christie: in One, Two, Buckle My Shoe, Mabelle Sainsbury Seale is actually Mrs. Albert Chapman, who herself is really Alistair Blunt's first wife, Gerda, who's been posing as his cousin! This is convoluted even by Christie standards.
The Westing Game: the entire point of the game is that one man has set up three identities named for points of the compass, and the winner is the first person to realize this and look for a fourth.
Fight Club: Tyler and the narrator. In fact, at one point, the narrator even wonders if Tyler and Marla are the same person, invoking this trope.
In Dragaera Kiera the Thief is also Sethra Lavode. In this case, the two characters share some common friends, but The Reveal is totally a shock because they seemingly have little in common, although once the reveal is made, clues in earlier books become noticeable.
In Gates of Ivory, Gates of Horn, by Tom McGrath, Cary and his nemesis/brother are different sides of the same person.
In the .hack// prequel novel AI Buster, the two main characters, Albireo and Watarai, turn out to be the same guy. The franchise does this a lot, actually, made easier by the characters' use of online aliases.
The Last of the Venitars takes this to the extreme. Tobias, James and the Beast are all revealed to be the same person, albeit in different time periods. Francis is also revealed to be "the old man".
Aragorn as Strider/Thorongil/whatever name he uses for adventuring and Aragorn as Elessar the Isildur's Heir in Lord of the Rings. There's no surprise for the reader, but in-universe not many people know they are the same person. Barliman Butterbur particularly is very surprised when he learns that the King who Returned and Strider the strange vagabond he knew are one and the same.
Gen is actually the Queen's Thief, Eugenides, revealed at the end of The Thief, the first book in The Queen's Thief series.
In Les MisÚrables, Jean Valjean is also known as Monsieur Madeleine, Ultime Fauchelevent, and Monsieur Leblanc which are both twists in-universe and out (although more so the former). Also, the Jondrettes later in the novel are revealed to be the Thenardiers.
In Warbreaker, it turns out that the infamous Kalad the Usurper who nearly started a world war, and the revered Peacegiver, who ended it were really the same person, who had become The Atoner, even though history thinks this was two different people. That person has many names, and is currently known as Vasher, and their "real" name (or at least the name they were given when they Returned) was Warbreaker the Peaceful.
For most of Thief of Time, even Lobsang and Jeremy themselves don't realize they're the same person. This one is more confusing than most, because they're the same person but have separate bodies (it's complicated).
In the first book of A Song of Ice and Fire, after being forced into retirement by Joffrey, Ser Barristan Selmy pledges to serve the rightful ruler and vanishes. A decent part of the next two books features various people vying for the throne wondering where the hell he went, until late in the third book he unmasks himself...on the other side of the world, where he's serving Daenerys Targaryen and has been for some time, under the name Arstan Whitebeard.
In the fourth book, Samwell Tarly briefly meets a girl called Cat. The reader knows all along that Cat is really Arya Stark, and that she is the sister of Samwell's friend Jon Snow, but he is oblivious to this.
Theon Greyjoy is knocked out at the end of Book 2, and then is missing for the next two books. Then in Book 5, a dirty, weak, and slightly insane character called Reek is introduced. Gradually, hints are made, until it is finally made clear that Reek is what is left of Theon after a year of physical and mental torture.
TinMan had a mild example when the party went to find "The Seeker" in the realm of the unwanted, who could guide them to Ahamo, one of the Queen's helpers. Well, yes, they are the same fellow...and that same fellow's third alias was the Queen's consort (and DG & Azkedellia's father).
Power Rangers RPM: It turns out that Tenaya 7 is Dillon's sister and was previously held captive as Subject T-78.
Kamen Rider Fourze does it epically as a major twist, with multiple layers that in one moment will change your understanding of multiple characters. How it looks:
The Big Bad, known only as "the man with red eyes" until we learn that he's Mituaki Gamou, kills Kengo's father in the backstory.
Virgo is The Dragon. Gamou's got three, but she's the most dangerous: The other two, respectively, have the job of recruiting new Zodiarts and being Gamou's bodyguard and only fight Fourze in the course of these duties. Virgo does one thing - she makes sure people who get in Gamou's way disappear forever. When she gets serious, Fourze is clearly outclassed in combat, and worse, she's usually able to reach her targets before Fourze can reach her.
Kuniteru Emoto, Kengo's dad's colleague, is an ally of the heroes. He's kind of nervous and clumsy, but smart. Having him around just might give them a leg up on finding out what's really going on.
Tachibana - no, not Tobei or Sakuya - is the mysterious masked boss of Kamen Rider Meteor. He lives on a space station.
How it is:
Virgo is actually: Tachibana and Emoto. Tachibana's mask deepens Emoto's voice, and Virgo is a reverse Samus Is a Girl; though not effeminate in any way, the male Prof. Emoto's monster form looks and sounds female. Male-seeming monsters have turned out to be female villains on many occasions - it works the other way around, too, for the first time ever. Emoto did work with Kengo's father... and eventually became jealous, betraying him, and... being responsible for the attack in the beginning that we always thought was Gamou because all we knew was that his eyes glowed red. As the ones who have been Zodiarts for the longest, Emoto and Gamou can both do Glowing Eyes of Doom. And that, my friends, is how a Wham Episode is done.
A very minor example in universe occurs in The Newsroom, Both Will Macavoy and Charlie Skinner have sources that told them about war crime committed by the US government, while the story was pretty much a go at that point Will's source cinches the deal and galvanizes the crew. Since the story is told via flashback the audience is instantly aware that they share the same source, but none of the characters realize that till it's much too late.
Doctor Who gives us a case where we see both identities, yet thanks to the huge span of time involved, we still have no clue that they're the same person until after The Reveal. The Face of Boe, a character introduced very early in the revived series, turns out to be a very distant future version of Captain Jack Harkness, a brief companion that first appears in a completely unrelated episode. When he turns up for The Master's storyline, it is revealed that due to Rose reviving him using the power she absorbed from the Time Vortex, he was accidentally made immortal. At the end of the story, instead of traveling with the Doctor to try and find a cure, he stays behind. He asks the Doctor about how aging will affect his appearance, mentioning that when he was young, his friends used to call him the Face of Boe due to his good looks. From there, the Doctor, Martha, and the audience connect the dots.
In Mass Effect 2, Shepard enquires to the location of her friend and ally Garrus Valkarian, only to be told that he disappeared a while ago. Not long after, she's sent to recruit an Omega vigilante called Archangel. Yup, one and the same.
In Umineko: When They Cry, it's heavily implied and later confirmed in the manga that Beatrice, Shannon and Kanon are all the same person; their true identity is Sayo Yasuda, who originally created them as "characters" that s/he pretends to be in order to cope with his/her low self-esteem and gender issues. However, in a twist on this trope, while these three characters are often shown interacting with one another to the viewer, the catch is that no one In-Universe ever sees them together outside of fantasy scenes.
In DuckTales episode "The Masked Mallard", there is the titular character of the episode gone rogue and a reporter named Lawrence Loudmouth bad mouthing him. It turns out he's the criminal.
In the sixth season of South Park, we meet Lu Kim, the Chinese owner of the Asian restaurant City Wok. Nine seasons later, one episode introduced Dr. Janus, who suffers a severe case of Multiple Personality Disorder. The same episode reveals that his strongest personality was none other than Lu Kim.
In season 2 of The Spectacular Spiderman, there's the Master Planner who is the Big Bad for a 4-episode story arc. He turns out to be Doctor Octopus, who's been pretending to be rehabilitated the entire time. He even explains the reason for this double-identity by stating that while Spiderman is looking for the Master Planner, he'll pay less attention to Doc Ock.
One of the famous Iga ninja is rumored to have done this to confuse his enemies, even going as far as having his subordinates pretend along with him (his alias was... a competing ninja leader in the same area).