Mobile Suit Gundam 00 has one in Season 2 Episode 14, when the identity of the 0 Gundam's pilot, as well as the reason/s for that scene in the prologue of Episode 1, is revealed to be none other than the Big Bad of the entire series, and that the armed intervention in question helped motivate his plans in the Second Season.
Pretty Sammy, Magical Project S: The whole show being a parody of the magical girl genre, you wouldn't expect much in the way of plot twists. Cue Episode 19- Sammy's Shrinking Violet best friend, Misao is really the sadistic Dark Magical Girl, Pixy Misa. More so, Pixy Misa is her default form; the shy and demure Misa was only a result of repressing her negative traits.
20th Century Boys: Friend iiiiiiiiissssssss *drum roll* Fukubei! Then comes along second Friend who is implied to be Katsumata.
In Code Geass, the secret behind Geass, as well as numerous other examples of this trope that pop up from time to time. Episodes 14 and 21 of R2 in particular are Infodumps on the nature of Geass and everything involved.
Naruto has been rather reveal-happy in recent years: we've gotten the true identity of both Akatsuki's leader and its Man Behind the Man, Kisame and Itachi's true motivations (including the real reason the Uchiha Massacre happened), the identities of Naruto's parents (everyone (and by everyone: the audience) knew about the father-it's the mother and her baggage that shocks everyone), the fact that Naruto is not the first host of the Nine-Tailed Fox, Madara really IS dead and Tobi's impersonating him, Tobi's current Sharingan sharing the same dimension as Kakashi's Kamui due to it being the right eye of Obito Uchiha, etc. And Tobi himself is later revealed to be Obito Uchiha. And now that There is a Man Behind the Man Behind the Man in the form of Black Zetsu, who finally succeeds to revive Kaguya Ootsutsuki, the mother of the Rikudo Sennin.
Vincent is the near invincible monster that was constantly tailing him and slaughtering everything in its way, the titular Ergo Proxy.
In the beginning Vincent was a Proxy, the near invincible monster tailing him was his clone-father's girlfriend.
Usagi/Sailor Moon is Princess Serenity. Although it could be made obvious over time—there are glimpses of the princess and she has the same voice actor—the original Japanese manga and anime didn't truly reveal this until well into the first season. The North American DiC dub, on the other hand, revealed this in the very first episode (or figured no one would put two and two together with the identical princess in a bubble and Serena).
Hagino's obsession with Mari in Blue Drop gets explained by revealing that Hagino saved Mari from drowning during the catastrophe caused by her space ship.
Hellsing: Dok was actually using the remains of Mina Harker as a template for all of Millennium's vampire soldiers. Turns out that since Alucard wasn't destroyed when he lost to Abraham Van Helsing, Mina wasn't completely purified of Alucard's curse. Thus all of Millenium's soldiers are poor copies of Alucard's power.
A big dose is revealed near the end of Spider Riders when the series Big Bad admits that he's a human. Not only that, he reveals that like Hunter, he was a hero chosen to protect the Inner World before he went nuts after his wife was killed.
First, Syaoran is a clone created by the Big Bad, and meet the real one.
Fai/Fay has a depressing backstory, he's faking his personality, is working for the villain, and he killed his brother. Then it's revealed that his memories were false, he didn't kill his brother, and he switches sides.
The whole goal up till that point, collecting the princess' feathers, was the Big Bad's Evil Plan to have her develop "physical memories".
The princess is a clone.
The original Syaoran is actually the son of an alternate version of the protagonist and love interest of Cardcaptor Sakura, and is using his father's name as a psuedonym. Then it's learned that the protagonist of Xxx HO Li C is a time-travel duplicate of "Syaoran".
And that the creation of said duplicate messed up the entire space-time continuum.
Then that "the country of Clow" is really Acid Tokyo in the far future.
One Piece has a number of them, many relating to the legendary Gold Roger. However, one of the most incredible was during the Jaya arc. Luffy gets into an eating contest with a random Boisterous Bruiser type guy at a bar, who later gives Luffy a pep speech in which he toasts to their shared ideals. Turns out that guy is Blackbeard, the evil pirate that Luffy's brother has been searching for.
Chapter 550 made another reveal. A reveal that doesn't make the plot take a new direction, but explained everything that has happened since chapter 1. Portgas D. Ace is not Luffy's biological brother; he's the son of Gold Roger, the Pirate King.
The reveal of who really attacked Iceburg in the Water Seven arc.
The reveal of what the ancient weapon mentioned in the Jaya Arc truly is in Chapter 649.
Chapter 731: Sabo is alive. It was only confirmed in Chapter 744.
Chapter 763: Trafalgar D. Water Law. Suddenly, his rapport with Luffy makes a lot more sense.
Chapter 816: The Minks really were sheltering Raizo, and were lying to Jack to the whole time.
A whole bunch in Chapters 817-820 thanks to the chapters being a huge Info Dump for the series' Myth Arc as a whole:
Kin'emon is not actually Momonosuke's father, but merely one of his attendants; Momo is a lord of the Kozuki clan, allies of the Mink Tribe, and his father Oden travelled to Raftel with Gold Roger. Both Oden and Momonosuke were/are also capable of hearing the "Voice of All Things", like Roger and Luffy.
Duke Dogstorm and Master Catviper traveled with Lord Oden after the latter left Wano: with Whitebeard originally, and then with Roger after the latter recruited Oden from the former's ship.
Raftel can be found by using four "Road Poneglyphs" that each indicate a separate location, with Raftel being at the crosspoint of the four. One of the Road Poneglyphs is in the Mink Tribe's possession, Kaido and Big Mom each have one, and the fourth's location is unknown. What's more, the Kozuki clan is the group responsible for making the poneglyphs.
The Witch Queen is The Faceless until the penultimate episode of the series (and only one or two hints are given to her true identity in the final season). She was watching the girls the entire time as Yuki-sensei, the school nurse.
Akatsuki is the prince of the Wizard World. This was so secret that even his best friends didn't know.
Ojamajo Doremi 16/17 reveals that Hana has a twin sibling. On top of that, Majo Rika and Majo Ruka are also twins, which makes their rivalry Sibling Rivalry.
Monster has a number of them, the biggest one probably being the reveal that the woman in Prague is really Johan.
Aizen didn't die. He faked his death, was the Big Bad behind the Soul Society arc and Tousen and Gin were his accomplices.
The Quincies still exist and have created a fully functional society living in the shadow of Seireitei. Literally. The two cities share the same space by virtue of a dimensional trick using Seireitei's shadows.
Masaki being a Quincy had been guessed by the fandom years ago, but she also turned out to be one of Aizen's Hollowfication victims. Ichigo inherited his inner hollow from her.
The name Yachiru means 'master of all known sword styles' and was taken by the monstrous First Kenpachi, creator of the 11th division, who is these days better known as Retsu Unohana, Captain of the Fourth Division Medical Squad.
The Quincies in the living world were wiped out in The Purge, The Emperor's attempt to destroy every "impure" Quincy. Ichigo and Uryuu's mothers were both victims of this purge and Yhwach's power flows through every Quincy alive, making all of them vulnerable to his whim.
Uryuu joins the Vandenreich, and is given the rank of Prince. Yhwach also tried to purge him but failed, making Uryuu the only impure Quincy alive and the only Purge survivor in history. Yhwach makes him his Unexpected Successor because he wants that power, knows Uryuu is capable of surpassing his strength, and suspects Uryuu wants to avenge his mother's death.
Old Man Zangetsu was only pretending to be Ichigo's zanpakutou. He's Ichigo's Quincy power, has been suppressing Ichigo's real Shinigami power, and is the image of Yhwach from a thousand years ago.
Pokémon does this with Pokemon's genders. For example, Pikachu, after ten years of debating, is proven to be male.
In Pokémon Special, Yellow is revealed to be a girl at the end of the Yellow Chapter (though Red doesn't find out until the Gold/Silver Chapter).
In Umi Monogatari it is revealed that Sedna is formed from the combined sorrow that the inhabitants of the island committed to the sea.
In Shaman King (at least the anime) the main antagonist is revealed to be the main protagonists Evil Twin.
In Tona-Gura!, Kazuki remembered that, even as a little boy, Yuuji was playful, and his 'perverted nature' is mainly him still acting like a little boy around his best friend. When he realizes that she * seriously* does not like it, and she stops romanticizing their childhood, things finally begin to move for them.
Mahou Sensei Negima!: Once the Magic World Arc starts, reveals are dropped left and right, especially once Kurt Godel shows up. The most important one is probably that Negi's mother is Queen Arika of Vesperina, making Negi a Warrior Prince. This is subverted when the girls discover that the Magic World is Mars and get excited, only to realize that it's just a useless bit of trivia. Then it becomes a double subversion when it turns out to be important after all.
In Soul Eater the killer of BJ was Justin Law. While not affecting the entire plot, it's still a major deal for certain characters, with potentially serious implications (if that one, who else has been overlooked?) in the series.
In chapter 72; Kid is said to be a fragment of Shinigami, who turns out to be one of a group of entities called the Great Old Ones. Making the Super OCD boy a Humanoid Abomination (currently) minus the evil and his 'illness' impliedly the result of the fact he/his father is an anthropomorphic personification of the 'madness of the rule of law'. Then in Chapter 108, it's revealed that Asura is also a fragment of Shinigami, effectively making him Kid's older brother.
In Martian Successor Nadesico, the Jovians are exiled humans victimized by Earth's government and who use the Super Robot series loved by the protagonists to justify destroying Earth. Also, the little girl the protagonist is shown with at the beginning is Inez Fressange, who is older than the protagonist due to a time paradox.
In Game×Rush, Yuuki's Mom/Yuki-san is Memori's presumed-dead birth-mother, who murdered Memori's father and supposedly died in the fire that Memori accidentally started (hence explaining both Memori's adopted status), but Miyuki did NOT die, instead wandering off with semi-amnesia to save a young Yuuki who was then raised as Memori (explaining how he knows so much about the REAL Memori). Bizarrely enough, due to the compressed storytelling and the changes forced by the same, it's possible for this to be not much of a Reveal after all.
The identity of Pride was revealed to be Selim Bradley.
Edward's automail arm isn't revealed until he foils an attack that would have destroyed a flesh-and-blood arm.
The Fuhrer is a Homunculus.
It's impossible to bring someone back to life. For anyone who sees the 2003 anime version first and then either reads the manga or watches Brotherhood, the shock is increased several-fold; in the 2003 anime, they're transformed into homunculi.
Magical Girl Lyrical Nanoha StrikerS. Protagonist Subaru, who has been a regular narrator ever since episode 1 (where as a little girl she is rescued by Nanoha and decides to become a hero too), finally battles the combat cyborgs but fails to rescue her sister and is seriously injured. Then her arm is seen. Along with the blood, metal and cables are seen. Subaru is a combat cyborg, too.
In Kirby of the Stars, there's a relatively minor one, compared to what's going on all around, but a reveal nonetheless. For 99% of the series, the Holy Nightmare Salesmen always appeared on the big screens in King Dedede's palace from the waist up. When Dedede and Escargo(o)n meet the Salesman face to face in Nightmare's fortress, there's the awful truth- All that's at the bottom are just kirby-like feet, no legs, nothing else.
The Distant Finale of Tengen Toppa Gurren Lagann reveals that the narrator speaking at the beginning of every episode is actually Simon in his forties. And in the second movie, during the fight between the TTGL and the Granzeboma, the Anti-Spiral drops the obvious (to the fans who've watched the anime) bombshell that if the Anti-Spiral is defeated, Nia will disappear. This shocks the Dai-Gurren Brigade and then the Anti-Spiral proceeds to tear the TTGL into many pieces, causes robot blood to spill all over the galaxy they were standing on. They got better.
In the last episodes, it was revealed that the Big Bad Silky who hates angels, is a 1/3 angel herself and has her fallen halo hidden in the drawer.
It was revealed that Mikael who was supposed to be an angel-in-training, lost his qualifications to become one and also hid his fallen halo in the boxes.
In the last episode, it was revealed that the whole plot of the show revolved around Mikael and not Noelle.
Tons of information revealed in Eureka Seven. Eureka's identity as a human Coralian, what really happened to Renton's father and sister, the origin of the 3 kids, the history of the Scab Coral which reveal that all along the planet was Earth which got covered up by a living planet-size alien. Gonzy was another hidden human Coralian.
Digimon has several. Hikari being the 8th Child and Tailmon being her partner, the fact that BelialVamdemon was behind everything in 02, Juri, after returning to the Real World, being an ADR, Duskmon being Kouichi, Kouji's long-lost twin brother, Kurata being a jackass and a Magnificent Bastard and that old guy being the head of DATS.
According to the Platonic Hearts rulebook, unknown and unmentioned until the very end, all losing contestants have their vocal cords removed and Mind Raped into idiocy before they get sold into slavery. Even the sympathetic ones. And you're shown the whole supporting cast in that pitiful state.
The almost unseen Cute Mute mom of Natsume? She's actually a Stepford Smiler, and a past contestant in the Platonic Heart martial arts tournament who managed to escape slavery and rebuild a semblance of normalcy before she hatched a complex Revenge by Proxy plan involving her offspring organizing the current edition of the Platonic Heart tournament to lure the daughter of the (still living) past winner and the (now dead) past promoter of the contest so Aya can relive every bit of her experience, including the defeat, maiming and slavery. She's also the daughter of the original organizer.
Aya's caring mom and her dead loving father? According to Miko and Natsume a sadistic Dark Action Girl and a sadistic rapist who had his way with the Action Girls defeated by his wife..
Although spoiled for U.S. audiences thanks to the fact that Dragon Ball Z almost entirely aired first barring a few episodes, in Japan Dragon Ball dropped a big one. In the manga, after Goku's big defeat of Piccolo, the following chapter features a mysterious character crashing to earth looking for someone named "Kakarot". And in the very last page of the chapter, Kakarot is revealed to be Goku. Then 2 chapters later it turns out that armored man is Goku's brother and Goku is revealed to be an alien. Piccolo and Kami get this same revelation not long after when they're revealed to be Nameks, which was foreshadowed as early as the 23rd Tenkaichi Budokai when the two spoke to each other in a strange language. It's done with Trunks as well. After his first appearance he's revealed to not just be another Saiyan, but a Super Saiyan as well, and just a few chapters later it's discovered that he's Bulma and Vegeta's son from the future.
Some of these examples are Eren being the Rogue Titan, the walls containing Titans, Annie being the Female Titan, Ymir being the Dancing Titan, Historia/"Krista" being related to a secret cult that knows about the walls, Reiner being the Armored Titan, and Bertolt being the Colossal Titan. Or the fact the basement contains proof that humanity was never wiped out and still exists.
Hilariously, one of the biggest reveals, the identities of the Colossal and Armored Titans, was revealed in just about the most casual manner possible, as part of a background conversation. Many readers (and watchers of the anime once it got that far) admitted to doing a Double Take as it took them a moment to process what they'd just read.
In Chapter 88, the Name of Eren's Titan is the Attack Titan (or the Shingeki No Kyojin).note The official Translation Attack "on" Titan is not entirely accurate. The translators were probably confused about that.
Black Butler: There are several regarding the character Angela Blanc. Firstly, they are not human, instead they are an Angel incognito, and a very evil one to boot. Also, a character that at first appears to be separate turns out to also be them, just in another form. Finally, they are responsible for the Phantomhive manor's destruction in the anime, and the deaths of Ceil's parents.
Magic Knight Rayearth: Emeraude didn't summon the Magic Knights to save her...she summoned them to kill her.
Kill la Kill has enough reveals to turn the fandom over its head and then back again.
Satsuki didn't kill Ryuko's father and played absolutely no role in his death. The real perpetrator is Nui Harime, who not only works for Satsuki's mom, Ragyo, but also killed Ryuko's father with the other half of the scissor blade, which she uses as her own weapon.
Life Fibers are actually sentient beings from somewhere in the universe and are the reason for why humanity has evolved from typical primates. And while the Life Fibers provide great intelligence and power, it turns out that inserting Life Fibers into a host would kill them painfully. However, the fibers can be worn, leading to the creation of clothing. Now, they are currently at rest under Revocs HQ, waiting for the time they can fully take over humanity and Ragyo has always been working toward that goal.
Satsuki and the Elite Four are actually working against Ragyo and her plans, meaning that they have been on Ryuko and Nudist Beach's side all along and simply kept to their own agenda.
Ryuko is actually Ragyo's daughter and Satsuki's younger sister. They both thought she was killed in Ragyo's failed attempt to fuse her with Life Fibers and was literally thrown away as a result. However, it turns out that the experiment did work and Ryuko's heart is completely made of Life Fibers. Not only that, but the reason that Ryuko survived being thrown away was because her and Satsuki's father managed to find her and escape from Ragyo. Ragyo tried to kill him, but he tricked her into thinking he was dead before changing his name and his appearance into the old man that Ryuko and the audience recognize as the father she's been fighting for.
Nui is also a human who was successfully fused with Life Fibers and her heart is shown to look just like Ryuko's. However, unlike Ryuko, Nui wasn't born in a mother's womb like a regular human but instead came directly from an artificial womb made of Life Fibers. So the reason she doesn't need to wear Life Fibers to be as powerful as she is is because she is entirely made of them.
Happiness Charge Pretty Cure had episode 20 and the reveal that Hime was the one who opened up the Axia Box, releasing the Phantom Empire. Two episodes later, it turns out that Iona's motive for revenge against Phantom was horribly skewed: her sister, a Precure before Iona, had been captured by Phantom only because Iona followed her into battle. And her capture was something she also blamed Hime on!
Noir: "Noir" is the legacy codename passed down by various pairs of female assassins trained from birth by an Ancient Conspiracy to become perfect killers. Kirika was a member of the current generation's Noir before her amnesia. Mireille is a failed Noir candidate, whose parents refused to give her up for training and were murdered for it—by none other than Kirika herself.
Madlax: "Madlax" was the codename of Margaret's father, whom she murdered in self-defense after he was driven insane by his arch-nemesis. However, Margaret possesses Reality Warping powers, which she instinctively used just before her patricide to create a Literal Split Personality—another seven year-old girl who pulled the trigger for her, so her primary self would remain "innocent". This other girl grew up to become the Madlax seen in the series, although neither she, nor Margaret retained any memories of these events.
El Cazador de la Bruja: Ellis is the only successful result of a CIA-funded program to artificially recreate a dying Witch Species. She did not kill her handler and father figure with her powers (as she believes), but was framed for it by the real murderer—the director of said program, who wanted to use her powers for his own goals.
There were several reveals in regards to Ugo. He was actually Solomon's djinn, not Aladdin's and his head wasn't missing like he had told Aladdin. He was unable to leave the "Room of Solitude". And as the flashback of Alma Torran revealed, Ugo wasn't a djinn at all but a genius magician, Solomon's closest friend and later became one of Solomon's three Magi.
Ren Gyokuen was the magi that betrayed Solomon. And she was Arba, Solomon's beloved friend and closest thing he and his lover Sheba had to a mother.
Anthy and Akio's true nature are major ones: They are in an incestuous relationship that resembles Domestic Abuse. Akio used to be Dios, a heroic prince that fell from nobility and became a Manipulative Bastard. He's also the prince from Utena's past as well as End of the World, the person organizing the duels. Anthy is a witch that was horrifically attacked for denying the world her brother and suffers constant torment as a result. She's an integral part of Akio's plans.
The castle in the sky where "eternity" dwells doesn't exist. It's an illusion created by Akio's planetarium projector as part of his hook to get people to participate in the duels. In fact, the entire hook is a lie: The duelist who wins the Rose Bride and the duels won't obtain the Power of Dios. The true purpose of the duels is for Akio himself to regain the Power of Dios, which he lost when he ceased to be Prince Dios. He just needs a powerful sword in order to break the seal on it- the winner's sword. To that end, he manipulated the young Utena into wanting to become a prince and gave her a duelist ring, hoping she would one day become noble enough to produce a sword that could break the seal.
From the Black Rose arc: Mikage/Nemuro's memories are fake- he's the one that burned down Nemuro Hall, not Mamiya. Also, the real Mamiya died years ago- the Mamiya we've seen with Mikage in the present is actually Anthy in disguise manipulating Mikage on Akio's behalf.
It starts out as a fairly run-of-the-mill slice of life show, albeit with a few odd details (who let someone keep their dog at school?). At the end of the first episode, we discover that the characters are in the midst of a horrible zombie apocalypse, and everything we've seen so far has been the product of Yuki's delusional lotus-eating. The strange details and inconsistencies are just side effects, and the other characters play along because they don't have the heart to tell her otherwise.
The reveal that Megu-nee has been Dead All Along is very different between the manga and anime. In the manga Yuki gets a massive headache and faints after being reminded of sometimes Megu-nee told her before her death. We're shown a flashback to Megu-nee's death and the next chapter confirms she's dead. In the anime the reveal happens chronologically later due to the series being In Medias Res. Miki is confused about who Megu-nee is so she innocently asks. This causes a creepy sequence where the background music is slowly warping and the scene pans out to show Yuki was talking to thin air.
In the manga Yuuri remembers she had a younger sister and goes hysterical with worry. She ends up risking her life to save a girl from an elementary school full of zombies however over the chapters it's shown that Yuuri is suffering from similar psychological issues to Yuki—the girl is really a teddy bear.
Scrapped Princess has a final twist reveal based on a single character's name: that Seria's last name is Mauser.
Midway through Your Name, it turns out that the "Freaky Friday" Flip is not in timed sync, and Mitsuha has been Dead All Along for three years after Itomori was destroyed in a meteor strike, killing five hundred people. The rest of the movie follows Yuki and Mitsuha as they attempt to avert this disaster.
In Izure Shinwa No Ragnarok, Raika's goal is to take revenge on the gods and rescue his sister from the one that kidnapped her. In the epilogue of Volume 1, it's revealed that his hyperactive classmate, Tenka, is his sister and the current host of the kidnapper.