The boss of the first dungeon level (Shrine Island) in Skies of Arcadia turns out to be an old and beat version of robotic guardians on Soltis, the sunken continent that Shrine Island is actually a part of.
In Fate/stay night, Gilgamesh shows up very briefly mucking about in the Prologue. Kuzuki also shows up briefly in the first day of the Fate route, and wouldn't go on to become important until halfway through the UBW route.
Similarly, the Avenger class is mentioned in passing as being something of a mistake that happens in the Grail War occasionally as well as the existence of Angra Manyu. These details aren't fully followed up upon until the sequel Fate/hollow ataraxia.
When you beat Garland as the first boss of Final Fantasy I, before the adventure properly begins, did you really think you'd ever see him again? And as the last boss, no less?
Krile in Final Fantasy V first appears as an illusion from the Siren, but Galuf can't recognize her owing to amnesia. She becomes a major character at the Earth Crystal when she pulls a Big Damn Heroes.
Final Fantasy IX has one of these in the form of an Easter Egg. When Baku is describing the plan to Tantalus on the ship at the start of the game, Zidane has the option of saying "That's when I kidnap Queen Brahne, right?" or "That's when I kidnap Princess Garnet, right?" Saying the "Queen Brahne" option a total of 64 times will eventually make Ruby come in and chastise Zidane, long before Ruby is ever properly introduced.
Zack in Final Fantasy VII is only mentioned off-handedly by Aeris/th, and an old couple early in the game, but of course he holds the key to figuring out Cloud's past. He's now considered important enough to warrant starring in a short anime and his own game, he even gets a last name (Fair). Even though anyone who's played FFVII knows how it will end...
And on the subject of Cloud's past, there's the Shinra soldier that is seen throughout Cloud's flashbacks of the Nibelheim incident. It turns out to be Cloud himself, as Zack was REALLY the one that was in SOLDIER and was Sephiroth's partner.
In Final Fantasy X a creepy and random child would appear every now and then, mainly forming in the main character Tidus' dreams. Eventually, he is revealed to be the Bahamut Fayth.
In Final Fantasy XIII, the first flashback (right after the party gets turned into Pulse l'cie) briefly shows an Amazonian Beauty having a drink and talking to Lebreau. All that's mentioned about her is that she's looking for someone. Later on, she becomes the Sixth Ranger of the group, one who was involved in Pulse's initial attack on Cocoon that started the whole fear of Pulse l'Cie in the first place.
Xenosaga Episode I features an Early-Bird Cameo of sorts for one of the major villains of Episode III, the android T-elos. Plans for T-elos are visible scattered around a U-Tic Organization battleship that Jr. and his crew storm. The mysterious young boy Abel also gets a split-second Early-Bird Cameo in the game's ending. Also, several scenes from Episode I's "8 Minute" trailer showcased key events like Jin and Margulis' epic sword fight and the unveiling of Proto Omega, which don't occur until well into Episode II.
Grand Theft Auto IV has this with the main characters from The Ballad of Gay Tony, Luis Lopez, and The Lost and Damned, Johnny Klebitz. Niko meets Johnny at a party and both are tasked with a drug trade that goes south for both of them. The main game deals with Niko's escape while Lost shows how Johnny escaped. Later Niko helps hold up a bank where Luis is taken hostage. Next Niko and Johnny meet up again at a smuggled diamond exchange at a museum, which also goes south when Luis shows up and shoots up the place. Each game deals with how they got out of there. Finally Niko and his friend Patrick exchange a hostage with Luis and his boss Gay Tony for the diamonds. Then in Lost Johnny has a mission where he sees Luis, Tony, and Tony's boyfriend, new character Evan Moss get the diamonds initially, and steals them.
Yusuf Amir was mentioned in a single mission in IV as a random real estate mogul Playboy X was trying to impress. Yusuf becomes a central character in The Ballad Of Gay Tony.
Similarly, Xemnas and "Terra"note We'll leave you to play Birth By Sleep by yourself to figure why "Terra" is in quotes. appearing as Bonus Bosses in the Final MixUpdated Rereleases.
Don't forget Aqua's armor and Keyblade in the Chamber of Repose within Hollow Bastion also in Final Mix.
In the beginning of the first game, a strange man in a brown robe appears and leaves some cryptic words. In the Disc One Final Dungeon, the robe man returns to possess Riku and reveals himself as Ansem. And then in Dream Drop Distance, it turns out that Ansem showing up on the Destiny Islands way back then was actually part of a massive time travel gambit, and his being there would later allow his younger self to travel to that point and enter the Sleeping Worlds to mess with Sora's head.
Xigbar in II was an entertaining, if forgettable, member of Organization XIII who mentioned once that he knew Keyblade wielders before Sora. Birth by Sleep reveals Xigbar may just be the only character in the entire series who knew everything that was going on. As Braig he worked for Master Xehanort, and when Xehanort got amnesia after possessing Terra Braig was the one who pushed him down the path to fulfill their plans.
In Persona 3: FES you can see most Social Link characters as well as Akihiko being pestered by fangirls during your character's first walks from the school to the dorm.
You can also meet all your school Social Links on the first day of school, and even talk to them.
Yukari and her Evoker appear briefly in a couple of shots in the first anime cutscene of the game.
There's also a non-character example: the music the protagonist is listening to on his headphones during that scene is "Burn My Dread -Last Battle-". This track later plays as a proper BGM (rather than being all muffled and distorted) during the final battle with Nyx.
Rise appears in the opening cutscene of Persona 4 in an advertisement before becoming a party member later.
The gas station attendant who shakes your hand at the beginning of the game turns out to be the True Ending's Big Bad about 70 hours of gameplay later.
Mitsuo is first seen asking out Yukiko on the protagonist's first day of school, and then isn't seen again until after he kills Morooka. Also, Nametame was first seen being mentioned on the news and can be seen around town. He isn't seen again until he kidnaps Nanako.
In Elite Beat Agents, sometimes, characters will pop up in stages prior to their first appearance. For example, Sam and Max (no, not ''that'' Sam and Max) appear in the "Rock This Town" stage, and Bill Mitchell, Tex and Amanda appear in "Sk8er Boi".
Used for hilarious results in OG Gaiden where Touma (Alpha 3 protagonist who has yet to appear in the series proper) appears as a Soba Delivery man, and in a voice acting joke, later on gets harassed by the Shura General Magnaz Ald, who happens to be voiced by the same seiyuu of his future rival Baran Doban (do note that Touma has yet to take a level in badass, so it is very plausible that he offers so little resistance). There's also Aqua Centrum (SRW MX protagonist) as a regular Federation soldier, in a Continuity Nod, Aqua says that she would never wear anything as Stripperiffic as Lamia Loveless' clothes. She's right: In MX, she wears even less.
There was also a Gunman in the Alpha series, in the first installment, you get to meet Mio Sasuga, one of the Elemental Lord heralds and she tells you to 'wait up for the next game', because she's going to appear. Guess what, she DOES appear in Alpha Gaiden (along with the rest of the Elemental Lords crews).
Also, in Super Robot Wars W, Yumi Francois, David Krugel and Natasha Pablociva from Tekkaman Blade II make an early cameo being visibly taken over by the Radam tree near the end of the first half, and later appearing in the second half as playable characters. They certainly didn't appear visibly (taken over off-screen) in the original first Tekkaman Blade.
In the same game, Mwu La Flaga, Gai Murakumo, and Yohko from Detonator Orgun all appear in the first half of the game as playable characters, even though their storylines technically don't even happen until the second half.
Baten Kaitos has one with an important villain for a good portion of the game being visible while the player selects his/her name and gender. This is later shown when the player witnesses the same scene as part of the story.
In Vampire: The Masquerade – Bloodlines, Jack, the first person you interact with, along with The Cab Driver responsible for getting the Main Character around Los Angeles, turn out to be responsible for everything that has happened throughout the game. The Cab Driver is even heavily implied to be Cain, the Father of all Vampires! Amusingly, if the player chooses to play as a Malkavian, this plot twist is Lampshaded during dialogue with some characters, though it is difficult to spot without having played through the game at least once.
This is the primary means of identifying people you can recruit for your army in Exit Fate.
In Dragon Age: Origins, an unnamed Circle mage at Ostagar objects to Cailan's plan to have The Warden and Alistair light the beacon for the army - and is promptly slapped down for his impudence by a nearby priestess. He turns out to be Uldred, a blood mage who later becomes the demon-infested stage boss of the Circle Tower.
And in Dragon Age II, during the first scene of Act I, an imperious armored woman with blonde curls glares down at a pickpocket as she passes by. Much later, she turns out to be Knight-Commander Meredith, head of Kirkwall's Templars and the game's Final Boss.
In Breath of Fire III, there's Peco, seemingly unimportant to the plot, with all his lines being pretty much comic relief. Then, out of nowhere, he saves your entire party from total annihilation simply because he's Yggdrasil, the Tree of Life.
At the beginning of Indigo Prophecy/Fahrenheit, we are introduced to a homeless man who watches Lucas flee the diner. If you talk to him as Carla and ask the right questions, he'll tell you his name is Bogart and he saw the "Devil, himself" leave the diner. At the end of the game, it turns out Bogart was the head of a secret organization of homeless people, battling the bad guys.
In Mega Man Battle Network 2, every so often, a gray haired kid who doesn't speak when you talk to him pops up in random places. Sure enough, he's the Big Bad.
Same thing happens with a certain Russian scientist in Battle Network 3...
Also, a possible subversion... In the Mega Man Star Force anime, as the FM-ians are outside the TV station ready to gate-crash Libra's show, Hope Stelar/Akane Hoshikawa (Geo's/Subaru's mum) is seen walking nearby behind them (And with an arrow pointing her out in a style similar to how every Chekhov's Gun in Ouran High School Host Club is pointed out). Amusingly enough, she DOES end up as a contestant in Libra's show and beats Cancer at it, but she ends up losing all importance afterwards.
Mega Man Legends: For most of the game, Data, the cutesy robot monkey, served as little more than a save point. Then, after beating MegaMan Juno, Data instructs Eden to call off its destruction of Kattelox Island due to Juno malfunctioning. It was as big a surprise for MegaMan as it was for the players.
The first meeting with Shandra Jerro in Neverwinter Nights 2 seems to serve no purpose and feels like filler. Then her grandfather becomes important to the plot. She's held Hostage for MacGuffin, is rescued, joins the party...
When players first meet Tabatha in Tales of Symphonia, they are quick to write her off as a background NPC, or if they are savvy enough a failed vessel for Martel. By the end of the game she fulfils her original purpose; hosting the soul of Martel and becoming the guardian spirit of the new Tree of Mana.
Likewise, Yuan. First appears prior to Kratos's first Face-Heel Turn, repeatedly, and definitely looks important. Remarkably, he manages to pull it off again in the second game, where he looks sufficiently different enough that you can't be sure if that's really him or not when you first meet him in Asgard, very early in the game. Right near the end, it proves to be him.
A bit of an aversion comes from the fact that many of the important characters have a theme song that plays when they show up, which kinda ruins the surprise if you figured that out early on.
In Red's Scenario in SaGa Frontier, Dr. Klein is connected to a Terrorist Organization known as Black X mentioned early on in the story, at the very end he says that he is the one behind everything. Not the case as the Real Leader is another being completely
Lang's assistant Shih-na, who barely says a word throughout the entirety of the case she first appears in, is Calisto Yew, murderer and The Dragon to the head of the smuggling ring.
Special mention goes to Misty Fey, who was only mentioned in passing at the beginning of the first game, then shows up as both major character and victim in the last case of the Phoenix Arc.
Honestly, there's always at least one witness that turns out like this, if not the killer himself. If the game is trying to keep you from paying attention to them, they probably did it.
Investigations 2 plays with this trope with Ryouken Houinbo. The first time he's introduced, Edgeworth is sure he's the killer, but he's not. Then you find out while he didn't commit the murder, he was pretty much the indirect cause of it. But just when you think you've seen the end of him... he turns out to be vital to the plot of the last case.
Also Sota Sarushiro, introduced in the same case as a seemingly wrongly accused person, turns out to be the Big Bad of the game.
In Wild ARMs 3, you'll occasionally notice a purple-haired little girl. She might just walk by for a second as you enter a town or dungeon, or show up standing near a plot-important character as he begins conspicuously talking to himself. She is, of course, the Big BadManipulative Bastard.
Of course, THE example in video gaming would be the G-Man in Half-Life who's seen in almost every level from the very beginning of the game in quick and silent appearances. Of course he turns out to be the most important character in the game.
Secundo, the Ambiguously Gay and Ambiguously Spanish AI from Beyond Good & Evil. He appears briefly in the first half-hour, then slinks back into the shadows, mostly just spewing pre-set lines... Of course, in the end, he's able to hack into the broadcast satellite on the moon and project the evidence of the Alpha Section's atrocities to all of Hillys.
Melchior in Chrono Trigger manages to pull it off twice. He's first introduced as a sympathetic merchant living near Medina, but turns out to be the only blacksmith capable of repairing the Masamune. Then it later turns out that he is one of the displaced gurus from 12,000 B.C.
The game's first boss, Yakra, is a great example of this trope. Although initially introduced as just a commander in Magus' army, and killed very early on, it is actually his defeat at the hands of the heroes that causes his descendant to seek revenge on Crono, by impersonating the Chancellor of 1000 A.D. and staging a fake trial, which ultimately pushes the heroes to escape to 2300 A.D. and learn about Lavos, setting the game's story into motion. What is amazing is that it is not until very late in the game—and in an optional sidequest—that you actually learn that the reason Crono was arrested and sentenced to death upon arriving home from 600 A.D. was not because the Chancellor was overzealous about Marle's safety, but because you "just" (well, 400 years ago) defeated a seemingly unimportant monster
Heck, Chrono Trigger requires its own folder for all of the examples of Chekhov's gunmen. There's the old man at the End of Time, who introduces the mechanics of time travel and magic to the party...and then, much later, we find out that he is Gaspar, the Zealian Guru of Time, and also creates the Chrono Trigger designed to reverse the flow of time to revive Crono after his Heroic Sacrifice.
Magus takes this concept Up to Eleven. He gets introduced as simply being the Big Bad of the Middle Ages, but his real significance to the plot is revealed slowly over the course of the game. He is revealed to be the reason why Frog is in his amphibian form, then we first meet him trying to summon the Final Boss. And then we meet him in 12,000 B.C., in two forms at once. He is conspicuously introduced as both a bizarre prophet who is using his own knowledge of the future to manipulate the Queen of Zeal, and the young Prince Janus (who is a Chekhov's Gunman in his own right), who is later shown being blasted into the Middle Ages, after (in his adult form) both he and the player party lose a Hopeless Boss Fight against Lavos. And then again, he is later recruitable.
Think you can pick out a Gunman just because of his custom sprite? Not so fast. Famously, Flea, one of Magus's generals, will first appear as a generic Juggler Enemy (coupled with a "Flea?" name during battle). It is until after the battle, however, that you learn that the true Flea has been there the entire time, as the tiny, generic little bat that's been following you since Magic Cave.
Several of the people at Millennial Fair can also qualify as Chekhov's Gunmen. Although they do not affect gameplay directly, helping/leaving them alone will help prove Crono innocent later on.
Speaking of which, The Trickster Norstein Bekkler is an inversion of this trope combined with a Guide Dang It: He appears as a special character, but is simply the introduction to several minigames, which have almost no impact on the actual game. However, later you are required to find someone who can produce a Clone of Crono to save the poor boy from oblivion. Guess who you have to find? Granted, you don't actually have to accomplish this task to continue with the game, but reviving the main character is kinda important.
Subverted in Chrono Cross: the element shopkeeper in Termina has virtually no plot significance, despite being one of a small handful of characters with portraits that aren't playable characters. In fact, there are plenty of characters who are more important who don't get portraits, such as the Chrono Trigger kids' time crash ghosts.
No One Lives Forever features a middle-age drunk civilian who appears in almost every level of the game. In the After The Credits reveal, he's shown to be the Director of H.A.R.M., and serves as the Big Bad of the sequel.
In Boiling Point: Road to Hell, a patron in the bar at the beginning of the game turns out to be The game's Big Bad. Because most of the people in the game are Signpost NPCs with identical dialogue, it's very likely you'll ignore him and miss out on talking to him entirely, and thus have no idea who the character is supposed to be when he suddenly becomes relevant to the main plot towards the end of the game.
The first few days in Persona 3 have over half the future Social Links making quick appearances.
True, but none of those pretend to be anything other than what they are, and players who are aware of the Social Link mechanic would naturally see any character they meet as a potential link. A better example is Ikutsuki, a conspicuously inoffensive character who is introduced early on, does next to nothing of note for much of the game (he's one of the few characters who fails to exhibit any obvious signs of a Dark and Troubled Past), and surprises absolutely no one when he turns out to be The Man Behind the Man.
In Persona 4, the gas station attendant, who is the third character you meet at the very beginning of the game in a seemingly throwaway appearance punctuated by controller vibration turns out to be the one directly responsible for everything that happens. You don't find this out unless you're on the road to the True Ending. This is also particularly well hidden because the player has been trained by this point to assume that anyone without a portrait is irrelevant to the plot — up until the reveal, the gas station attendant only has a normal, inconspicuous character model. He only gets one afterThe Reveal.
Made all the more effective by the fact that while players will note the vibrating controller, plus the fact that the MC feels nauseated after meeting him, the game is so long, plus the fact that any other contact you can have with the Attendant are the optional mini-conversations that you can have with any other NPC, that most players will forget about meeting him at all before the first in-game month is out!
In a smaller sense, Naoto Shirogane only appears as a relatively minor character just before the second dungeon, and later becomes your final party member. Then there's Taro Namatame...
Don't forget Rise Kujikawa, who appears in a short commercial in the beginning then later becomes your support character.
As well as Adachi, who is ultimately revealed as the murderer despite being a mere inept detective up to that point. The game's main plot practically runs off of this trope.
Captain Wesker in Resident Evil fits this quite well. He poofs off at the start of the game and then turns out to be the Big Bad of the entire series, except for Resident Evil 4. Kind of.
The zombies in the Remake of Resident Evil for Nintendo Gamecube become this if you fail to dispose of their bodies properly. If you think those zombie bodies just lay there the rest of the game to avert Everything Fades, you're in for a nasty surprise when they start getting back up about an hour later.
Chris Redfield and Jill Valentine also qualify. In Resident Evil: The Umbrella Chronicles, Claire mentions that she had never expected to use her brother's training whilst in zombie-occupied Raccoon City, meaning that she learned how to survive from him. In Jill's case, being infected with the T-Virus and surviving thanks to Carlos producing an antidote in Nemesis isn't that big of a deal...until it is discovered after tackling Wesker through a glass window before Resident Evil 5 that her bloodstream held a rare strain of T-virus antibodies which Wesker uses for his Uroboros research.
You can now add Sherry Birkin to the list. Like Jill, she has G-virus antibodies following Claire curing her in Resident Evil 2. Fifteen years later her own antibodies are used by Carla Radames to perfect the C-virus.
In Conkers Bad Fur Day, the three cavemen punks you see in the Rock Solid level standing next to the giant keg serve only as decoration. You later see them again when they mug you and challenge you to a hoverboard race. Ironically enough, the fourth member that you don't see in Rock Solid is the one that falls off his board and dies.
Malak's former master Darth Revan is shown in flashback a couple of times, only for others to mention that Revan is dead now. They're wrong however, since Revan is also the player character.
In Star Fox Adventures, The Hub Level has one Thorntail that doesn't speak to Fox, grumbling that he's tired. Turns out he's the fourth and final Gatekeeper.
Stage 2 of the Touhou game Perfect Cherry Blossom features the nekomata Chen as midboss and boss. She is written off as an unhelpful nuisance, like most bosses before Stage 4. In the Extra Stage, she returns as the midboss - she's the shikigami of Ran Yakumo, the Extra Boss and herself shikigami to Phantasm Boss Yukari Yakumo.
But wait! It gets better with Kogasa in Undefined Fantastic Object. Surprise!And again in Ten Desires!
In Subterranian Animism, the cat miniboss in Stage 4 turns out to be Orin, the main boss (AND miniboss) of Stage 5. And she shows up again as the miniboss of the final stage.
In Disgaea: Hour of Darkness Mid-Boss starts out as a speedbump and doesn't get much better. Sure, he can pick up Flonne's holy pendant without getting burned, but that's probably because he's too lame to actually be evil. At the end of the game, it turns out he's the spirit of King Krichevskoy, Laharl's father, who's been working with the Seraph to test if Laharl is ready to be the Overlord.
Earlier in the game, the castle's monster occupants show up to save your underleveled butt after it gets kicked by an Alternate Netherworld monster. Before and after that they're pretty much decorations.
In the third game, Geoffry seems minor, but he's the Big Bad of the game.
Ryuji Yamazaki was introduced in Fatal Fury 3 as a Psycho for Hire under the Jin twins. In the later series The King of Fighters, it was revealed that at least some of his madness is caused by his Orochi blood; he's a member of the Orochi clan central to the main plot in The King of Fighters series. Subverted somewhat in that he just doesn't care.
Paper Mario: The Thousand-Year Door played this trope pretty commonly. Of note are Flavio and General White, who both debuted at least five chapters before they were needed. Another example is Goldbob, who appeared in several chapters in different locations with his family before his major role. The game had a running gag about Mario running into several unimportant recurring characters each time he arrived in a new locale, and Goldbob blended in perfectly.
The original did this with Parakarry.
In the original Super Mario Bros. game, killing the Fake Bowser with fireballs at the end of World 3 will actually turn him into a Buzzy Beetle. Buzzy Beetles actually do not appear until World 4-2, and unlike the one mentioned above, cannot be killed with fireballs.
Another example is the first Fake Bowser, who is actually a gray Goomba. In the final level, all Goombas there are colored gray.
Ghost Trick has a habit of making the most innocuous characters turn out to be extremely plot-relevant. This includes Missile, who comes back as ghost and ally in chapter fourteen and Ray, who makes The Dog Was the Mastermind literal, but the most egregious is that black cat who shows up in the junkyard for two seconds. Not only is that the Big Bad possessing the cat's body, but the body is Sissel's actual corpse.
In Red Alert, every so often, a bald, goateed man appears and tells Stalin various things, though players don't get to hear his lines. Then the ending appears, and you realize said bald, goateed man is quite the Magnificent Bastard.
Paladin's Quest has Duke, a party member who only stays with you for roughly the first five minutes of the game. He turns out to be Zaygos, who was using you to awaken the destructive creature Dal Gren.
In The Spirit Engine 2, you can see the Big Bad walking through the background in Chapter 3, if you keep your eyes open and know what to look for. Also, later on, he makes a brief stint as Mr. Exposition.
Subverted in Grandia II by Tessa, who might fool you into thinking she may be recruitable, or secretly a bad guy, but is in fact neither and dies for real within 10 minutes, despite having a VA and profile picture.
In the DS game The World Ends with You aka It's A Wonderful World, a slightly different sprite can be seem in a crowded scene at the beginning of the game, chillin' and not even having a line. Or moving. Or doing anything, for the matter. He's in fact the fourth main character, and the one who set up everything in the game to happen.
Mother: Cognitive Dissonance gives us Zarbol. He joins the party just like everyone else to find the pieces of the Apple on Enlightenment and keep them safe from Giegue and that's about it. He is actually Buzz Buzz from EarthBound, sent back in time to give Ness a warning about the threat of Giygas.
Mother 3 gives us Leder, the incredibly tall, silent guy standing by the bell at the start of the game who you probably ignored, and later disappears without a trace following the time skip. Turns out that he was entrusted to be the only one to retain any memory of the events that lead up to the settlement of civilisation on the Nowhere Islands, and thus, he was imprisoned by the Pigmask Army in hopes that no one would be able to learn the truth. Who knew?
The Kid in Jak II: Renegade isn't just the lost heir, he's Jak's younger self. Also, Veger may have kicked Jak out of Haven, but it wasn't personal... except he knew that Jak was the little kid, he knew who Jak's father was, and he was responsible for separating the two of them in the first place.
Amy of the Soul Series first appeared in a minor role in the Attract Mode of Soul Calibur II hiding Raphel from Guards. She returns as a playable bonus character and Raphel's main motivation in the next game, revamped for the arcade version into a full character and then revamped again for Soul Calibur IV as a full character.
Also, Algol in Soul Calibur IV; he's been mentioned as the "Hero King" who created Soul Calibur in pretty much every game beforehand, finally getting a fully-playable reveal in IV.
The Blood Omen Series has a brilliant example of this. Janos Audron is only a passing detail of flavor text in one of the items' descriptions in the very first game of the series, never mentioned anywhere else. He reappears to be a mentor to Raziel in the second game, then we learn that his species, of which he is the last specimen, are actually ancestors to the vampires of this universe.
In Metroid Fusion, Samus mentions that her new ship's onboard AI reminds her of her old CO, Adam Malkovich, who had died. It turns out that he actually is Adam, revealed when he says Something Only They Would Say.
In Star Control II, a player's very first encounter will most likely be with a "drone-vessel" of the Ur-Quan. When you talk to them, in the corner of the screen is a small, frog-like animal which translates for them. It's there just to add flavor, right? So very wrong, as they later turn out to actually be the Dnyarri, an ancient race of evil psychics, who enslaved the Ur-Quan ages ago. The Ur-Quan have since rebelled and managed to free themselves, then proceeded to take their revenge by turning the Dnyarri into mindless animals. An "awakened" Dnyarri has a rather major role in the game.
In the Story Mode opening for BlazBlue: Calamity Trigger, one scientist offhandedly refers to the failed subject eleven. Guess who becomes one of the playable characters? Less offhandedly, you have Tsubaki Yayoi and Hazama, who start as NPCs but are playable in Continuum Shift.
And now we have Makoto Nanaya and Valkenhayn via DLC.
Fire Emblem is full of these, often in the form of characters giving you items in villages, and even in the houses scattered about the battle field. One example in particular that stands out is the Bishop Renault, first encountered giving you a small item in one of the early chapters. Turns out he joins the party in the last two chapters. Furthermore, you can find out via support conversation that He murdered Lucius' parents, was Wallace's battle instructor, and he was Nergal's Guinea Pig in developing his morphs.
There's also Finn from Genealogy of the Holy War, who was fairly unimportant in the First Generation but comes back in the Second Generation and in Thracia 776 as a father-figure to Leaf and one of the figureheads of Lenster's liberation movement.
Path of Radiance has one too: In one of the early chapters, in which you rout a bunch of pirates from a port, there is a house you can visit with a man that gives you an Elixir. That man is none other than Nasir, who just so happens to be a rather important character in the game, as well as a pretty decent unit to play with.
Then of course, in that same game, there's Zelgius, who seems like some dude in Begnion's army, but turns out to be none other than the Black Knight himself in Radiant Dawn!
Another one from Path of Radience: Izuka, a major antagonist in Radiant Dawn, makes a brief appearance in one of the last chapters of the game.
In Shadow Dragon, There is an out of the way village you can visit while conquering Gra. There you'll meet a man with a unique sprite and the name "???" who'll give you a Thoron tome and tell you to pass it on to Boah (who you've rescued from Archenia palace). Several chapters later, you have a chance to fight him in Grust, where you find out he's General Camus, the man who was in charge of Archenia palace until he allowed (read: helped) Princess Nyna to escape. We also find out that he and Nyna love each other, although this is not enough to get him to switch sides. He also shows up again in the sequel disguised as "Sirius". You recruit him in an early chapter, and you need to take him into the final battle if you want to save Nyna
In the Game Boy Color game Magi-Nation, there is one who is practically a Chekhov's boss. In the third Shadow Geyser, you are suddenly stopped by someone named Warranda who summons a creature (and is practically a joke boss) She says a few things to you and then vanishes...making you wonder what the point of that was (unless you didn't return the Key to Ashkar). Then in the fourth Shadow Geyser, she appears to be the guardian of it, but gives you an offer. She'll either give you the Plot Coupon and let you go without a boss fight (making it the easiest Shadow Geyser after the first one) or you can fight her. If you take it and leave, you'll seemingly avoid a boss battle. HOWEVER, if you do this, in the fifth shadow geyser, she mysteriously appears out of nowhere and tells Tony that he promised to leave, and didn't, so it was time to fight her. (Whether or not she's more powerful at this point isn't really known)
In Killer7, while running through the early stages your character is constantly being contacted by a man named Johnny Gagnon, his messages arriving by carrier pigeon. This wouldn't be too unusual if he didn't address every letter to someone named Emir and wasn't writing about the Smith syndicate you play as. Later, you learn about a man named Emir Parkreiner, who is the most important character in the game and the murderer of the Killer7 in their past lives. It would make sense that Emir hired Gagnon to get information on the seven assassins so as to have some intel on his targets.
In StarCraft, we have Duran, the ghost who betrayed the UED and disappeared sometime during the Zerg campaign of Brood War. Turns out he's been taking the alias Narud in Wings of Liberty seeking Xel' Naga artifacts and is in league with the true Big Bad of the series, the Fallen One.
World of Warcraft has a bunch of characters like this. Some of the more notable cases include:
Tirion Fordring, who made his debut in the Eastern Plaguelands all the way back in the original release. Here he was a disgraced former paladin who gave you a couple of quests, culminating in him taking up his sword again. Two expansion packs later, he shows up again as the Supreme Commander of the Argent Crusade and is one of the most important characters in Wrath of the Lich King. His shiny new levels in badass come complete with his own unique legendary blade pulled straight from the Expanded Universe and a few one-on-one battles with no less a figure than the Lich King himself.
Gryan Stoutmantle, a low-level questgiver who hangs out in Sentinel Hill in the original content and leads the Westfall Militia. Come Wrath, he's been upgraded to Captain Gryan Stoutmantle, leader of the Westfall Brigade and commander of the Alliance's military efforts in Grizzly Hills.
In the Pandaren race's Noob Cave there's a character named Jojo Ironbrow, named so because his head can break virtually anything, and sends the player to gather bamboo, wood, and stone so he can demonstrate. When you help Ji attack a Hozen village, you find a jade statue, itself a Chekhov's Gun, that is the only thing he can't break, so he uses it as a battering ram to knock down a gate near the end of your quests, and he later follows Aysa to Stormwind when she joins the Alliance.
In Tales of Legendia, the first time Senel encounters the Bantam Bouncers, you can spot someone who has a unique model in the bottom of the screen - it's actually Grune, a later party member and is pretty much God.
Fallout 1 doesn't so much have a Chekhov's Gunman as it has a Chekhov's town. The game's First Town is a quaint little village where you perform a few mini quests like giving pointers to the town farmers, clearing out a nearby radscorpion den, helping create an antidote to radscorpion venom, and dealing with the local Raider threat. This small village goes on to become the New California Republic, one of the most powerful and influential factions in the setting.
The second Pokémon Mystery Dungeon game features Torkoal, the local elder, who the heroes meet at a hot spring at the end of Waterfall Cave. He turns up again when the heroes and the guild need a lead on where to find the Hidden Land; being the oldest Pokemon in Treasure Town, Torkoal supplied his old wisdom to the guild, and thanks to him, they managed to find where it is.
Drowzee, the second boss and first outlaw that the main characters arrest. In the post game, he helps the main characters get into Azurill's nightmare after being let out of prison and being sorry for what he did to Azurill before.
Arley, Hocus, Kasa, and Edward from Pokémon Ranger: Guardian Signs. They are introduced at various points in the game, Arley and Edward are introduced at the beginning. The player dismisses them as pointless NPCs. Towards the middle of the game, they all gather and have a tea party. Towards the end of the game, they raise a giant fortress into the sky, and they destroy the island that they player started out in. It turns out they were controlling the evil group of the game, and they wanted to take over the world. They are the final bosses of the game.
In both of the Gamecube Pokémon games, you meet a stout and kind old man 15 minutes into the game. They are the leaders of Cipher, the crime syndicate terrorizing Orre, and they are the final bosses of their respective games.
After Gen I, it's almost tradition for the champion to be some seemingly innocuous trainer who has almost no ties to the plot whatsoever aside from occasionally aiding you against the regional villain team, only for you to find out the truth when you go to face the champion after defeating the Elite Four. The only champion to ever subvert this was the champion of Pokémon Black and White, Alder. That was most likely deliberate.
The Legend of Zelda: Majora's Mask has an example that only pays off in the ending credits. Remember that creepy withered tree near where Link is cursed into Deku Scrub form? Remember how, if you take the "chase the Deku Butler through the maze" sidequest, he'll mention that you remind him of his son? The credits shows him sitting in front of that tree, grieving.
The Happy Mask Salesman is a minor NPC in Ocarina of Time. In this game, he becomes a major character, and one of his masks getting stolen is the catalyst for the whole plot.
In ''Twilight Princess, the game's first miniboss Ook the Monkey appears after Link frees him from the influence of an Insect of Darkness to help Link in the second phase of the fight against Diababa by swinging around carrying Bomblings for Link to hurl at Diababa with the Gale Boomerang.
Dr. Harlan Fontaine in L.A. Noire only appeared in some newspaper flashbacks where the early ones usually showed him doing seemingly innocuous things. It turned out that he was one of higher up members of the Suburban Redevelopment Fund which was responsible for the events of the Arson section.
Janos Audron is mentioned in precisely two lines in Legacy of Kain: Blood Omen, presumably to never be seen or heard of again. Two games later, he became a major character and the main driving force behind the Big Bad's actions.
The Orion Conspiracy introduces you to a tough female pilot named Brooks. She seems to have only a small role in the game. Later, she gets killed off trying to stop a berserk Ward and LaPaz drags her body out of the corridor. Later, when you get to the shuttle, you find out that the NavCom chip was destroyed, effectively crippling the shuttle. However, LaPaz reveals that there is a backup chip...located in Brooks's brain! Squick, but it does explain why LaPaz dragged Brooks's body out of a corridor that had to be sealed shortly afterwards.
At the very start of Guild Wars Prophecies, you meet a friendly, innocent 10 year old girl named Gwen. You can talk to her and she will follow you around. If you give her flowers and a new flute, she will even give you a tapestry shred as a sign of friendship. Then the Searing happens and Ascalon is destroyed, ending the tutorial and beginning the game for real one year later. Gwen is not mentioned again, although you can find a broken flute and a torn girl's cape, implying she had been a victim of the Searing. Two full follow-up games and an expansion pack later, you meet up with Gwen again, now 8 years older and a cold-hearted, ass-kicking Mesmer, after spending years as a slave. She goes on to be a major character in the Eye of the North expansion pack and the subsequent Guild Wars Beyond missions.
As a bonus, the tapestry shroud she gave you kicks off a quest where you go on a mission with her to find, you guessed it, the flute you gave her 8 years ago. Chekhov's Gun, indeed.
Heihachi Mishima. The guy locks up his dad, tosses his son into a ravine, adopts another kid which becomes his first son's rival, and guns down his grandson. Yeah, it's safe to say that Heihachi's actions drives the series.
In Fallout: New Vegas, while optionally talking to your boss at the courier agency, you can find out you weren't the first pick for the Platinum Chip job that got you shot. The first guy for the job, a fellow named Ulysses, saw your name on the list, forfeited it and said you should have it. In the DLC's, particularly Lonesome Road, he turns out to be...rather important.
Mass Effect 1 has a sidequest in which Shepard has to deactivate a rogue Alliance VI that has apparently achieved sentience. Very late in Mass Effect 3, it's revealed that the AI was actually a very early prototype of EDI, the Normandy's artificial intelligence in the second and third games and a squadmate in ME3.
Another optional sidequest involves an asari diplomat hiring Shepard to rescue her sister who was kidnapped by mercenaries, which turns out to be a ruse to manipulate Shepard into killing her since she was blackmailing the former. The diplomat, Nassana Dantius, shows up again in Mass Effect 2 as the focus of Thane's recruitment mission where we get a better glance at how bad she is.
Sindel falls under this trope as well. Revived by Quan Chi's necromancy, later powered up by Shang Tsung's soul by Shao Kahn, which leads her to slaughter her daughter and most of the Forces of Light, with Nightwolf killing both him and Sindel in the process.
Mario & Luigi: Partners in Time used Toadbert, an amnesiac Toad from the present who was one of Peach's bodyguards. After the Shroob Mothership, Kylie Koopa falls on his head, which causes him to rush to the Bros. to tell them that he has the fifth Cobalt Star Shard, but the Cobalt Star Shard won't defeat the Shroobs. His efforts to stop the Bros. are in vain thanks to the Elder Shrooboid.
Sand whales in Serious Sam 3 are typically just a form of Border Patrol to prevent players from wandering out into the open desert. The final boss area is in open desert, and the final boss is the size of a sand whale. Hence, he will often challenge the whale when he gets bored with you, giving you a chance to shove metal poles into his back.
In the first level of Max Payne 3, Bachmeyer, Becker, Da Silva and Dr. Fischernote in the magazine Clue show up, well before they're formally introduced.
The love interest from Sigma Star Saga is the first boss (it's pilot, anyways).
In the Sega Genesis version of the Animaniacs game, Pinky and the Brain can be spotted as one of the many cameos throughout the game. However, in the first stage, in a blink-and-you-miss-it moment, you can find the two building a suited robot. It's the game's final boss.
Skullgirls held a campaign which showed a number of characters that could be potential playable DLC characters, and out of the 32 potential options, 30 of them had appeared in the game previously in one way or another, either as major characters, NPCs in story modes, and/or background characters on stages and cutscenes.
In Batman: Arkham City, during the intro where you control Bruce Wayne, a prisoner standing in front of him on a line will say "You're dead, Bruce Wayne...you're on my list". Since he looks somewhat nondescript and everyone else is hurling threats at Wayne, you tend to ignore him. He's actually Floyd Lawton AKA Deadshot, the focus of a sidequest chain.
In The Halloween Hack, Apple Kid mentions he hasn't heard from Dr. Andonuts since Giygas was defeated. Guess who's responsible for all the monsters?
Danganronpa has two gunmen, Genocider Syo and Alter Ego. The first is brought up at the start of the game as the possible mastermind behind the cast's current predicament, and later on turns out to be Fukawa's Split Personality, while the latter is revealed during Chihiro's third free-time conversation to be an AI he created, and after his death it's revealed that he uploaded a copy onto a laptop they found earlier.
In Three The Hard Way, several random NPC townies you can interact with may reveal themselves as a Kaibutsu Lord
Syphon Filter 2 introduces Chance as an unassuming Red Shirt G.I., but at the end of the game, he is revealed to be an Agency mole who was calling the shots behind Logan's back the whole time.