According to fanon (and a few fan-made addons) he became Nerevarine's companion in the quest. Also, in the Elder Scolls IV: Oblivion, asking certain characters about rumours will reveal that Jiub has become a saint in Morrowind. And why? Because he drove the Cliff Racers out of Morrowind. Hell yeah.
They also say that he was killed by the Daedra during the invasion.
Jiub was soul-trapped and killed by a Dremora during the Siege of Kvatch. How do you know this? Jiub tells you in the Soul Cairn if you get the Skyrim DLC, Dawnguard. Yep, he's back.
Another Morrowind character that disappeared was Caius Cosades, the first major quest giver of the main quest. He was supposedly recalled to Cyrodiil during the main quest, but is not seen in Oblivion at all.
Lore texts written by designer/developer Ken Rolston seem to indicate that Caius is alive and well following the Oblivion crisis.
King Helseth is another character who vanishes from the lore after the events of the Tribunal expansion. He apparently remained King until at least the events of the Oblivion crisis, but there is no word on his fate afterwards. Unusual for the series which likes to give at least subtle hints as to the fate of prominent characters from past games in future ones.
The fourth case of Phoenix Wright: Ace Attorney: Trials and Tribulations revolves around a murder committed during the hostage exchange of Dahlia Hawthorne for a two million dollar diamond. Much is made of the fact that Dahlia Hawthorne's corpse disappeared along with the diamond after the murder, but while the former is found easily the latter is never recovered. One could assume Dahlia sold it, but that doesn't explain why the thief doesn't have two million dollars sitting in their bank account somewhere and it's not brought up again.
The first game caused an accidental disappearing mouse. In the fourth case von Karma makes a throwaway reference to having a child whose seven year old daughter has a dog named Phoenix. In the second game we meet his daughter Franziska, who does not have any children, nor is old enough to have a seven year old one. While this was probably not intended, many people are left wondering who the mysterious older von Karma sibling is.
Of course, Von Karma could just be lying. It wouldn't be his first lie.
Evidently it was confirmed that Manfred does have an older daughter, who is the mother of the granddaughter he mentions, but that still doesn't explain why we never hear anything else about her.
There is also the missing 4th clue from the final case in Justice for all, that Franziska took with her abroad and promised to return to Wright when they meet again. She never did give it to him in the next game Trials and Tribulations.
In the third case of the first game, Sal Manella disappears after his testimony, and is never mentioned again after Phoenix mentions that he helped Dee Vasquez move the body.
He gets a brief cameo in the first Investigations game, but it's still never mentioned what happened to him between case 1-3 and then.
Chrono Trigger, where the fate of the character Schala is unexplained/occurs off-camera. The resurfacing of the subplot in Chrono Crossmay or may not have been planned beforehand.
A better example is what happened to Magus, Schala's brother. In Chrono Cross, the character Guile was supposed to be Magus still searching for his sister but Square dropped it during development. There are still several scenes from the game that Square left in from this plotline. The most obvious is a letter from Lucca that suggests that Janus (Magus' real name) was travelling with you. Of course considering what happened to the rest of the cast from Chrono Trigger this might be a good thing.
In the new DS game, Magus, upon the realization that he could never be strong enough to deal with the Time Devourer, casts aside his memories and winds up in a forest. What happens to him from there on the other hand...
In Chrono Cross, the scene where Kid declares that Terra Tower has assumed its true form, after which nothing is ever mentioned of it again. It just floats there menacingly for the rest of the game.
In Zelda: The Wand of Gamelon, Princess Zelda is constantly accompanied by her nanny Impa, who mysteriously vanishes near the end of the game and is simply never seen, heard, or mentioned again.
The entire premise of The Legend of Zelda: Majora's Mask is that Link has been detoured from his quest to find Navi. After he saves Termina Tatl says that he should get back to what he was doing. This raises two questions. How does he get back to Hyrule, and did he ever find Navi? Neither is answered, but at least we can assume that the Happy Mask salesman helped him get home. But Navi is never mentioned again.
Gabe's story is continued in the Dawn of War books, although he ends up dealing with Necron and Chaos, rather than the demon.
The real cause is an unfortunate round of Executive Meddling attempting Status Quo Is God. In this case, Gabriel was such a popular character that GW has introduced him into the official background lore of the game as Chapter-Master of the Blood Ravens... and hence he can no longer be used in the Dawn of War games because it would mess up the lore.
Actually this has all been resolved as of the latest Expansion pack to Dawn of War II, Retribution set a decade after the events in Chaos Rising Long story short, the now corrupted Chapter Master/Chief Librarian Azariah Kyras makes an Epic Face Heel Turn and turns half of the Chapter to Chaos, in the Space Marine campaign it's revealed that although Ulkair was responsible for allowing Kyras to Go Mad from the Revelation it's the Maledictum Deamon -the same one that Gabriel released in the first game- that turns him to Khorne and leads him to slaughter millions for the Blood God so he can ascend to Daemon Princehood, in the last mission Gabriel goes one on one with the Daemon Price and promptly get's his ass kicked, though thanks to the Player Character he survives and in an Awesome Moment of Crowning is named Chapter Master in the final cutscene of the Space Marine Campaign.
Magical Starsign has a pretty odd one; at the Starfall Festival event, a breather not-quite-cutscene, you can wander around and talk to the individual members of your party. The event only ends when you talk to Mokka the robot (if the player character is a girl) or Lassi the rabbit girl (if the player character is a boy}. They're just about to admit to being in love with you, but your clueless Heroic Mime will be hijacked by another character and poor Lassi/Mokka will confess their feelings into thin air. Before and after that, nothing. No further acknowledgement, nothing in the epilogue. Cue a massive "Huh? Why was that even put in there?" on the player's part. It could just be part of Magical Starsign's odd humour, but the nature of the scene hints that this development has a significance the game never gives it.
This issue pops up with Pico and Sorbet's blooming romance as well. It's pretty obvious that Pico is in love with Sorbet, and in one cutscene, they have a touching moment together, but Pico drops out of the academy, and Sorbet becomes part of The Space Police and that little subplot remains unresolved.
Leafos' family history in Viva Piñata looks like a plotline, but it never actually goes anywhere. You should, for example, be able to work out that Stardos is now Dastardos, and Leafos alludes to this...but you can't really do anything about it, or even receive further clarification beyond unlocking the diary entries as you level up. There's no way to bring the dysfunctional family back together (maybe you wouldn't want to...) no matter how good your garden in...and despite the long, involved history in the diary that seems to indicate that their problems are intrinsic to the game.
Corporal Adrian Shephard is the protagonist of Half-Life: Opposing Force. At the end of the game he gets Put on a Bus by the GMan, who was impressed at his survival skills. Cue Half-Life 2, and Shephard is the only character who has yet to make an appearance. Valve has recently gone on-record saying they've noticed how much of a fan-favorite he is on account of how vocal the fanbase gets about this particular mouse, so we might see him again.
Opposing Force was developed by Gearbox Software, so Valve may not own that character or may not consider him canon. The Race X enemies haven't reappeared either.
The Final Fantasy series has notoriously bad continuity as far as sidequests go.
Banon in Final Fantasy VI. He starts out as leader of La Résistance against The Empire in the World of Balance. He is never mentioned in the World of Ruin. The most likely explanation is that he died in the apocalypse, but this is never confirmed.
Seigfried takes that amazing treasure from the phantom train, practically right out of your hands... but certainly we can get it back in the World of Ruin... right?
In Final Fantasy VIII, the big bad is defeated and all of the characters live happily ever after; everyone seems to have forgotten that the city of Esthar is still overrun with monsters from the Lunar Cry. Attentive players will note that the Lunar Cry is a recurring natural disaster, but that's only a flimsy justification.
In Final Fantasy IX, much of Freya's backstory concerns her search for her lost boyfriend, Fratley. She finally finds him again about a quarter of the way through the game, only to discover he has amnesia. He then heads off before Freya can say much to him. Typically, one would think that he would reappear later and the plot would continue when he does, but no, it never happens. He appears again in the ending sequence (still amnesiac), but this seems like a hastily-added attempt at covering up the planned-but-deleted sidequest.
Also in Final Fantasy IX, a very well hidden quest reveals Garnet's childhood name, to the amazement of the cast. And then it's never mentioned again.
In Prince of Persia (2008), the main character begins it by losing his donkey, Farah. He's wandering around, calling for her when he runs into the princess. Although she is occasionally referenced Farah is never seen.
It is later explained in the credits of the EDC for the game. Farah the Donkey is dead, but the developers assure us that no real donkeys were harmed.
A comedic example in Fallout 2; you can take up a short treasure hunt, which culminates in lowering a treasure-hunting dwarf down a well to retrieve a bag of loot. It turns out to hold a fortune in bottlecaps, the now-worthless currency of the previous game. After cursing, kicking a bit of dirt and ultimately having a good laugh about it, you head off again, leaving the dwarf stuck down the well.
A possible fate of Follows-Chalk in Fallout New Vegas if you convince him to leave tribal life to see civilization for himself.
Quite famously within the fandom, you never do rescue Sulik's sister, find Sulik's village, or any trace of the slaver group that kidnapped her.
What was with Kamyu's blood drinking, spirit talking and... other nighttime activities, anyway? Presumably they were supposed to be foreshadowing for Mutsumi but... she didn't do any of that stuff either. And it's not like the original her even could have done anything like that. Plus, isn't Mutsumi Hakuoro's surrogate daughter? It seems doubtful that she would do anything like she did if she's supposed to be being influenced or something.
Resident Evil has a very bad habit of doing this. Rebecca, Billy, Carlos, and all the characters in Survivor and Dead Aim never have their fates revealed aside from "they survived". Barry, Hunk, and Sherry run very close into this, only having the epilogues in 3 reveal some things about what happened to them. In a nutshell, if you're in this series and your name isn't Chris, Jill, Leon, or Claire, the plot doesn't really give a damn about you.
Literally done in Resident Evil Code Veronica. Twice in the game, Claire runs into a mouse (first hidden in a locker, the next in a secret room). In the unlockable minigame, you have a chance of finding the mouse's diary explaining everything that happened to him.
Midway through Prototype, Alex's sister Dana is kidnapped by The Virus; Alex manages to rescue her from the epicenter of the outbreak, and drops her off with Doctor Ragland. Considering that Dana Mercer and Ragland were pretty much the only sympathetic characters in the entire game, the fact that neither one is seen again is a bit jarring.
Dana shows up again in Prototype 2, no worse for wear. Ragland's still unaccounted for.
Alex's fate is deliberately left unknown at the end of Golden Sun: The Lost Age. The fandom looked for his return in Dark Dawn. They delivered. He hid himself as Arcanus the whole time, but Kraden forces Alex to reveal his true identity near the end of the game.
Speaking of Dark Dawn, Psynergy Vortexes are a significant part of the very early plot, but you never hear one whit about them after you get Rief out of his box cage. That is, until the quest is over, the initial trio return to the Goma Plateau, and Matthewpoints out over the horizon...
At the very beginning of Shadow Hearts, Yuri gets his arm ripped off and is able to reattach it, and it heals instantly. He never manifests this power again, and its origin isn't explained.
In the same sequence, Alice is shown to have a pendent which somehow repels evil spirits. We never see or hear about it again. She repelled the evil the pendant wasn't actually important.
The sex scenes in Kanon suffer from this. They happen and then they're never mentioned again (beyond the screen immediately afterwards), even if the follow-up scene would warrant a mention. Particularly glaring in Shiori's and Ayu's scenarios, where one of the characters reminisces about everything they've done together and mentions everything except the sex. Makes it kind of easy to make the clean version, huh?
In The Godfather, The Trojan is an original character who serves as one of your hit contractors. Unlike the various other original characters, most of whom are killed onscreen, he plain disappears after giving his last contract hit and doesn't receive any closure as to his ultimate fate.
Some extremely vague dialogue from Pete Clemenza suggests that The Trojan is working at cross purposes against the Corleone Family. This only comes about if you accept several missions from The Trojan and neglect Clemenza's contracts; at one point, you find Clemenza in the compound basement shooting empty beer bottles acting very upset. Only the farthest limb on the Epileptic Trees connects this to the character's actions, though.
Made more strange by the fact that in The Trojan's last hit he says he will be accompanying you, but he never shows up. A probably unrelated character named 'The Trojan' is on the family tree in the second film listed as being in prison for drug peddling so this may have been his fate.
Frank Pentageli's fate is left out of the sequel. You'll have to turn to the film to find out.
What was with the game of kick the can in Ever17? Blick Winkel and time travel don't explain that at all. Despite the Mind Screwdriver of the True End route it's still not clear what was going on there.
The true identity of the bodies discovered on Mt. Akakura in Remember11 is never revealed. They are initially presumed to be Kokoro, Lin, and Yomogi, as those three were the only unaccounted-for passengers of a plane that crashed in that area, but the true end reveals that the three of them survived.
Although Yuni implied that the newspaper with the article itself was fabricated.
MOTHER 3 gives us the Egg of Light. Early on, you retrieve it from the Osohe Castle, without its purpose explained. Then, while you're escaping the castle, you lose it, and only find it a few chapters later...at which point it never affects anything again. Its purpose is eventually explained in a late-game spoiler, but it's never used for that purpose.
This is a side-effect of Shoot the Shaggy Dog. When the Pork Army failed to get their hands on the Egg, they kidnapped Leder, the only person who knew what it did and how to use it. With him out of the picture, even if the village got the Egg back, it would be useless to them. By the time you actually meet Leder, everyone is already in New Pork City. Even if it were used to give the villagers their memories back so they would all fight Porky, they are far outnumbered by the brainwashed people Porky kidnapped through time. They wouldn't stand a chance. The only thing left to do is for Lucas to pull the final needle and see what happens.
In the World of Warcraft expansion pack Wrath of the Lich King, a val'kyr (undead valkyrie) named Annhylde the Caller shows up at the end of the Utgarde Keep dungeon to revive the boss Ingvar the Plunderer as an undead. After that? She vanishes, and does not appear again. However, in a subsequent short story centred on Forsaken leader Sylvanas Windrunner, it was later revealed Annhylde sacrificed herself to keep Sylvanas alive.
This is not surprising if you have played as a Death Knight. During the starter quests, a Val'kyr will typically help you once or twice after you die in battle and not be seen again. However, Annhylde's fate is revealed in Sylvanas's short story; she is one of a few surviving Val'kyr and gives her life to revive Sylvanas after her suicide.
In Burning Crusade, we meet Sabellian, a black dragon who helps the player defeat a Gronn. He survives the battle and disappears afterward. Two expansions later, the Fangs of the Father questline is centered around helping the uncorrupted black dragon Wrathion eliminate the rest of the Black Dragonflight. Despite Wrathion claiming to be the Last of His Kind at the end of the questline, Sabellian is neither killed nor mentioned to be dead, leading some to believe he may have survived. Of course, it's also possible he died offscreen and the player just doesn't find out.
A recent Ask CDev briefly addressed this, saying that Wrathion is the Last of His Kindas far as he knows, but also points out that Wrathion is not all-knowing, implying Sabellian did indeed survive.
Goriona, Warmaster Blackhorn's twilight drake mount in the Dragon Soul raid. She helps Blackhorn during the Skyfire battle, but abandons him and flees once her health gets too low. Despite explicitly surviving the encounter, she's not seen or mentioned again afterward.
Many quests and NPCs were removed in the Cataclysm expansion, even the ones not overtly affected by Deathwing's re-emergence.
The leaders of the non-playable factions in World of Warcraft often suffer this fate. Even when there is a specific gathering of the major leaders, these guys often remain absent. Notable examples are Roanuk Icemist (leader of the taunka), Danath Trollbane (leader of stromgarde), Rexxar (champion of the horde), elder torntusk (leader of the revantusk trolls), Velog Icebellow (leader of the frostborn), Arechron (leader of the kurenai) and greatmother Geyah (leader of the mag'har).
The entire nation of Kul Tiras. Even the fleet that got referenced as scouting Kalimdor vanished without mention somewhere after vanilla. Kul Tiras is an especially notable example, since every expansion has featured at least one appearance by a human-led fleet, but there has been no sign of tirasian forces at all, despite it being their hat. We don't even know the name of the current lord-admiral(their equivalent of a king), and we have no clue whether or not the cataclysm affected it.
As far as worgen players are concerned, the worgen storyline drops off the face of the Earth after the worgen player completes the starter zone and is shipped off to Darkshore to become a night elf with fur. This also overlaps with Obvious Beta in that the continuation of the worgen story only appears in quests that are exclusive to the other faction; to see the whole story, the worgen player would have to reroll a Horde character. The Alliance version of Shadowfang Keep references the events of the Horde-exclusive storyline, causing many an Alliance player to wonder who Ivar Bloodfang is, why he thinks Crowley is a coward, and why he wants the suddenly back from the dead trio of Godfrey, Walden, and Ashbury killed so bad.
There was a rumor that he was originally supposed to be killed by crashing a plane into his building, which was removed for obvious reasons after 9/11, but this has been debunked.
The last mission you "do" for him—Donald's Disappearance—is only for the purpose of showing you that he's gone.
Subverted in Super Metroid. Samus can meet very friendly little animals in the game, including three monkey-like creatures and something resembling a dodo, both of which demonstrate new abilities she can do that aren't mentioned elsewhere in the game. As you escape after setting a time bomb powerful enough to blow up the entire planet, which would naturally kill them, you can take a very brief detour to the room where you initially found the Bombs and find them trapped there, where you can use your newly-acquired BFG to blast open a wall and free them. Of course, that fails to address how unintelligent animals like that escaped the explosion of the planet that occurred moments afterward. They appear in the later game Metroid: Fusion, but no explanation is given as to how they survived.
It is established in the ending of Metroid Fusion that they are intelligent enough to use (at least basic) ship commands. When an Omega-stage Metroid attacked Samus's ship in the docking bay, the ship's computer could not get out of the station by itself since the autopilot was not activated. Later it revealed to Samus that these lovable critters helped it taking off and then re-entering the station when the battle was over.
If you save them, you can see them flying off in what is assumed to be their own ship after the planet blows up. In Metroid Fusion you find them on one of the decks of the station, so it's assumed that either Samus brought them there for testing (since she was working with the scientists) or they were caught and taken there separately.
It's generally assumed to be the latter, since Samus' dialogue shortly after releasing them in Fusion implies that she hadn't known of their fate.
This has been a topic of discussion since the beginning of Tekken 3, just where is Jun Kazama? Her son Jin's entire motivation from the game he debuted in was to avenge his mother's "death"; the problem is in fact that he actually never saw Jun dying, and only assumed that after she stayed to fight Ogre as he ran away the God had her killed, (although the wrecked and burnt surroundings from the place she was fighting was a good indication). This doubt still persists in the 6th game of the franchise by adding more uncertainty in Jin's assumption on Jun's death, and the fact that Word Of God refuses to say she is dead doesn't help either.
Actually, Jun being alive is a plot point which Namco have deliberately kept a mystery for dramatic effect. It is likely but unconfirmed that it will form a major part of the story later on in the series. The reason Asuka is in Tekken 5 is to be a scrappy for Jun so that (nearly) all the characters who were in Tekken Tag would be playable (in some form) in Tekken 5, as Namco had received a lot of flak for not including them in Tekken 4, people obviously missing the point of Tag being a compilation game and not a canonical sequel.
Given that both Asuka and Jun are in Tekken Tag Tournament 2 and Jun has a direct connection to the boss of that game, it's now painfully clear that Asuka is not and never was going to be a replacement for anybody. Remember, too, that even if a Tekken fighter was dead, that doesn't mean that person is dead now... Bryan Fury, anyone?
And what happened to Kunimitsu?
It seems to be implied that she is in hiding—she stole from her tribe and Yoshimitsu presumably wants to kill her. In the non-canonical Tag he actually does kill her in one of the endings. Some of her moves were carried over to Raven, as well as Yoshimitsu.
Kunimitsu, available in the console ports of Tag 2 as DLC, was excommunicated from the Manji Party after her failed attempt to steal Yoshi's katana, thus affirming the above. Her whereabouts and what she's been up to for all of these years during her exile remain a mystery.
And the biggest mystery of them all, Kuma's second costume in the first two games is a polar bear. From the third onwards, (where Kuma is replaced by his identically named son) his second costume is another character, Panda. Nobody knows what happened to polar bear Kuma and it's never been mentioned.
"Polar Bear Kuma" was simply an alternate Palette Swap rather than an additional character. That's like asking what happened to the Heihachi who wore nothing but a bandage diaper.
Alex? Okay, he's marginal at best, but if Mokujin could make the cut for TTT2...
Granted, Mokujin's bio in T5 explains that he (re)awakens in response to great evils (Ogre in 3, Jinpachi—or more specifically, the devil controlling Jinpachi—in 5, Azazel in 6). Alex seems to have just fallen off of the face of the earth, which is made even more puzzling by the fact that Roger not only has a family (his wife and son appear as a duo starting in T5), but Roger himself is still alive and kicking as of T5 and ''T6
Well, Alex is back (as DLC) for TTT2, so it's a start.
In Valkyrie Profile: Covenant of the Plume, there's the question of Natalia's lost children. They're strongly implied to be Enfants Terrible Mischka and Mirielle, but the matter is never direct addressed, nor does it have much apparent bearing on the plot. Even though they meet on two of the game's story paths, and Mischka and Mirielle kill Natalia in one of them.
The first Valkyrie Profile has an odd version, because you know what happens to the character, but no idea how. Lawfer's recruitment cutscene doesn't show or even allude to how he dies, but he ends up one of your Einherjar anyway once it's finished. The manga has him turn into a vampire and get killed by Arngrim, but this doesn't fit with the events of the game.
And early in the game, during Belenus's recruitment scene, Valkyrie comes across a name and keeps it in mind, yet we never see this vampire she was talking about.
Psychonauts: Wait... did Crispin get out of the insane asylum too before it exploded?
She plays a major role and her fate is revealed in the downloadable mission pack as Subject Sigma's main ally. Although it's doubtful this was planned ahead of time so much as when they started writing the story for the mission pack, she was now simply conveniently available.
The Beetle is introduced at one point in Spider Man 2 Enter Electro as one of Electro's goons, as well as a potential boss character. After his initial appearances he's never seen or heard from again.
In Persona 3, the next-to-last boss is Takaya, whom SEES defeats to the brink of consciousness, but doesn't outright kill. He spends the entirety of the Nyx Avatar fight unconscious, then comes back to laugh in the party's face when Nyx itself is bringing The Fall to Earth. He collapses in a fit of laughter at the very top of Tartarus, the Protagonist does his thing, Tartarus (and Nyx) goes away... and nothing is ever said about Takaya ever again, even though he didn't die and was just as invested in the proceedings as anyone else who had the power of Persona.
Then again, He is dying because of the drugs he was taking, and after the battle everyone loses all knowledge of the Dark Hour and everything that happened in it. So he probably died while everyone forgot who he was.
Cave Story: The Korons. Their kidnapping is a major motivation for their adoptive mother, Curly—until the Core fight, after which Curly never mentions them again. *
Granted, most of this can be explained by her being amnesiac or too busy trying to save the world; but in the final cutscene she's neither of those.
While the Korons themselves do get rescued by Momorin and Itoh, there's no logical way that Curly could know this.
Jack's fate is implied rather than shown: He's in the Plantation jail along with Sue, then he's gone by the time the plot forces you to get thrown in jail. The implications aren't pretty. However, it's possible to completely skip seeing Jack in the cell, rendering his disappearance from the game rather more baffling.
Star Ocean The Second Story: A rather large (if technically optional) aspect of the first part of the game involves you finding an ancient text in Cross Cave and showing it to a linguist named Keith. Keith finally takes it and begins studying it, but before you learn anything about it, the world explodes. You never find out what was actually in it, making several long-winded events and dungeons seem annoyingly pointless.
It's revealed in Bowman's solo ending that the text is a myth about an 'ancient paradise' called Nede.
In the original Star Ocean it's strongly implied that Marvel is actually Ioshua's missing sister, and you later find said sister's body in seeming suspended animation — in fact, one of the big clues to Marvel's identity is how strongly she reacts to this discovery. However, there is no way to actually confirm that Marvel is said sister or restore her to her original body, so nothing ever comes of it. This was finally addressed in the PSP remake.
The Sims had a lot of these. Sims 2 had Bella Goth, who was later lampshaded. She slept with her daughter's fiancée and ran away because she was ashamed, according to EA. For a long, long time there, and yet she seemed like such a big character in the original game (and seems to be a mascot, of sorts, too). A more prominent example, from Sims 2 DS, is Mayor Honest Jackson. After Ava waltzes into the hotel, he completely disappears. He still calls your character with requests and romantic options, though, most of which cannot be fulfilled because he's not there.
Discussed in Metal Gear Solid Peace Walker. Big Boss rides into the Costa Rican cloud forest on a mule, but encounters enemies who spook the mule and he runs away. While most of your support team is focused on the mission, the younger two, Paz and Chico, are more concerned with what happened to the mule. (It doesn't show up again.)
A really bad case of this happen in Scrapland. Through the game, three important city officials are murdered and have their "matrix" (which allow them to be resurrected) stolen, effectively removing them from existence, the goal of the protagonist is to investigate the case and find out who's responsible. However, even after you find and defeat the guy responsible for the plan, what happened to the victims's matrix isn't addressed in any way.
For a long time, Ys had this in form of Raba. (or pick your preferred romanization) Appearing in the Very Definitely Final Dungeon of the original game and playing a decently major role in clearing it, the last we see of him he's wounded, but not mortally so, and he could easily have survived or died. He doesn't appear nor is mentioned in Ys II, and Ys III ends up taking place in a distant land. What happened to him was finally addressed in Ys: The Ark Of Napishtim... 5 games and 16 years after his first appearance.
What happened to Dogi during V?
In Lufia II: Rise of the Sinistrals, Maxim's childhood friend Tia is the second member of your party. Tia clearly loves Maxim, and follows him on his journey for this reason, despite his cold behaviour towards her. Later, the party meets Selan, who Maxim is clearly interested in. The game appears to be developing a rivalry between Selan and Tia, which one might expect to end with Maxim finally realizing his own true love for Tia, but instead Tia suddenly decides she's had enough and leaves the party, never to be heard from again except in a small scene at the end.
Lufia And The Fortress Of Doomdid establish he had to end up with Selan eventually, but there were probably much better ways to resolve that than having Tia suddenly decide to vanish from the face of the earth.
Maxim was actually just not romantically attracted to Tia at all. Tia's case was more like unrequited love toward Maxim - he just did not want to be bound to a life as a shopkeeper, and he preferred to be with a warrior like himself.
Tia actually stays in the remake, Curse of the Sinistrals, and remains a viable part of your team throughout the whole game. She even starts dating Dekar!
In First Encounter Assault Recon, the player character starts out partnered with a man named Jankowski. Very early in the game, Jankowski disappears, but starts appearing to the protagonist as bloody apparitions throughout the rest of the game. It's highly likely that he was killed by Alma, but no explanation is given for why his apparitions keep following the character, nor is there any conclusive evidence regarding his fate.
Word Of God confirms he is dead, but they wanted to make it a bit more mysterious, hence why his vital signs keep showing right throughout the game, though with "some kind of interference" Given how powerful Alma is, pretty much nothing is out of the question.
Towards the very beginning of Banjo-Tooie, a couple of characters mention how excited they are about "the upcoming kickball game between the Jinjos and the moles": indeed, it's the main reason Jingaling wants to see the Jinjos rescued. The game is never mentioned again.
Also, Klungo from the first game. He only appears during the scene where Grunty is shown building the machine she will use to suck the beauty out of Banjo's sister, after which he disappears and is simply never seen, heard, or mentioned again. The only time you ever see him again is if you lose the game, where he actually succeeds in turning Grunty beautiful... at least, until his brief appearance in the ending sequence. He gets an expanded role in all of the other Banjo games, though.
And of course, how could we forget about Tooty? You know, Banjo's little sister? The one whom Grunty wanted to steal her beauty from and thus started the events of the entire series? The one whom her older brother Banjo cared enough about to search a creepy witch's lair, climb tribal mountaintops, swim towards shark-infested islands, get swallowed by a giant sewage-machine, wade through piranha-swamps, freeze his arse off in the North Pole, then burn his arse off in a desert, investigate a haunted residence, nearly drown in a polluted shipyard, time-travel through a sky-high forest, win a literally-fiery gameshow, and beat said witch who started it all, JUST to get to her? And then suddenly never even see her again in the series (save for an in-joke missing picture on a milk carton in Tooie, and other references)? What? You say you don't remember? At all!?... hehe, me neither. Kazooie must be his new real sister by now or something...
In the first level of Halo: Reach, Noble Team comes across a young Hungarian woman named Sára. The game bothers to name her, give a short but personal conversation between her and Jorge, and connect her to a moderately important NPC, and then she is never seen or heard from again. According to lead concept artist Issac Hannaford, she was originally intended to have a much bigger role (namely, as Noble Team's science advisor).
In a series-wide example, we still don't know what happened to Jun; he doesn't even get a mention in the 2010 reprint of Halo: First Strike, despite being last seen escorting Halsey, one of the most important characters in the entire series.
For the forces that battle the Yellow Turbans in the first act (nearly all of them), if you play it in its entirety and then allow Zhang Jiao to escape at Yellow Turban Rebellion, you will not kill him, and you also will not get the Return of the Yellow Turbans special stage, the only other stage he shows up in. You're left with only the assurance that the threat of the Yellow Turbans is over, and Zhang Jiao just quietly fades from history. (I suppose you can assume that he succumbed to disease, since that's what actually happened.)
You cannot under any circumstances kill Dong Zhuo at Hu Lao Gate. Meaning that unless you're playing as Lu Bu, the only way to see his demise to get the one of the "Dong Zhuo Lives!" special stages or the "The Symbol of the Mandate" special stage. Therefore, it's very likely you'll finish the entire campaign without ever learning Dong Zhuo's fate. (Similar to Zhang Jiao, you can assume that Lu Bu eventually whacked him.)
If you're playing as any force other than Wei, Lu Bu, Dong Zhuo, or the Yellow Turbans, you will face Lu Bu exactly once, at Hu Lao Gate, where it's not possible to kill him. He's never mentioned again. Presumably Wei takes him out, but you only get to see this if you're playing as Wei.
Also as Wei, you face Yuan Shao at The Battle of Guan Du, where he'll retreat if things go badly enough. If you didn't meet the requirements for the "The Esteemed Yuan Family" special stage, that's it; he's gone for good and presumably becomes a footnote to history. (THAT, at least, doesn't require much imagination!)
Lu Bu, Yuan Shao, and Dong Zhuo have a single battle against each of the Three Kingdoms. Only two of them are required. How Cao Cao, Sun Jian, or Liu Bei knuckles under to your iron rule without a fight is left to your imagination.
As Wu, it's possible to get Race For The Nan Territory, where both you and the Shu army battle a total of four Wei generals, after Wei has already been destroyed. Since none of the four die in this battle, it's unclear what becomes of them afterward, or for that matter what the hell they're doing here in the first place.
In Lego Batman, a cutscene shows a man preparing to propose to his girlfriend. When he produces the ring, the girl screams and ducks under the table. The man is sad, not realizing that she screamed because Joker and Scarecrow were coming up from behind him in their aircraft. The man is swept up by the planes and is last seen clinging to a steeple. Did he ever get down? Did Batman rescue him? Did his girl say yes?
In Time Crisis: Project Titan, not only is Kantaris alive, she appears in a couple of cutscenes. She doesn't die, or for that matter fight anyone. And she has not been seen, heard, or mentioned in any Namco game since. (For that matter, does the fact that she's alive mean that Richard Miller failed his special assignment in TC1?)
It's stated in the game's epilogue files that he was killed off-screen during the final mission... why how climatic.
At the end of World 5 of Super Mario Galaxy 2, Bowser Jr. is blasted out of his malfunctioning Boomsday Machine, and is simply never seen, heard, or mentioned again afterwards.
Also, if you attempt to fight Bowser with Yoshi at the end of the final level, when the second phase of the final boss battle commences, Yoshi mysteriously vanishes and is simply never seen, heard, or mentioned again.
It should be noted that the only way to actually have Yoshi with you during the final boss is through a glitch which allows infinite jumps while riding him. Therefore, the game is just taking away something you shouldn't have in the first place.
In Paper Mario The Thousand Year Door Despite both directly controlling Bowser throughout the game, and him and Kammy being main characters in the story, the two are never mentioned in the "Where Are They Now?" Epilogue that shows Gombella's e-mail where she tells Mario what everyone is up to. The last time Bowser and Kammy are ever seen in the game is lying in defeat before the final boss after your boss fight with them, and they vanish after you leave the room and are never mentioned during the ending at all.
In Super Paper Mario, upon first meeting Dimentio, Tippi recognizes him instantly. How she knows him is never explored any further. Even in their spoilerific backstories, there doesn't seem to be any mentioned reason as to why she would know him.
In Puzzle Quest 2 after you gain Rahn the guardsman as a companion (gaining the Besiege spell), you never hear from him again. He has no dialog, unlike your other companions. And when you rescue your companions from Dark Elf Arena, he's not even mentioned.
Odium: The last you see of Anna Hutchens and another team member (Medusa or Slavsky) is when they are left behind before the last level because the team leader decides it's too unsafe for them beyond this point. They are never seen or mentioned again. Especially jarring with Medusa (the mutant who retained his sanity)—was he ever turned back into a human, or at least re-integrated into society, or... something?
Then there are the two random robbers who don't seem to be afraid of all the biomechanical monstrosities roaming around. Your team scolds them, takes their loot (which consists of nothing except for a journal... kind of low ambitions these robbers have) and sends them on their way. You never find out what happened to them afterwards, or how did they get into the town and survive so long in the first place.
At the very beginning of Home Front, you are arrested in your home by a KPA colonel named Jeong, who seems like he will be a significant antagonist. He appears exactly one other time in the game, leaves, and is not mentioned again afterward.
Command & Conquer: Tiberium Wars adds a third side to the GDI/Nod conflict with the Scrin Alien Invasion. Whatever campaign you choose, the Scrin discover that Humans Are Warriors and are chased off the planet, planning to return in greater force. They are never heard from again.
Legend of Dragoon reveals in the third disc Shana is the twin sister of the dead Princess Louvia, which makes her daughter of Queen Theresea and heir to the throne of Mille Seseau. This is never mentioned again or even touched upon for that matter. Many found it to be a glaring plot hole.
Kano is last seen frozen by Cyber Sub-Zero, but not shattered. He just disappears from the scenes, although apparently he did warn Quan Chi of Cyber Sub-Zero.
Cyrax and Sektor may or may not be dead.
Also, Raiden mentions that he sent Liu Kang and Kung Lao to rescue their Shaolin Masters near the beginning of the MK2 part of the story. It's never mentioned if they succeeded or not.
Given how a lot of the info in All There in the Manual, Mortal Kombat suffers from this frequently. For example, it's been brought up in bios that the Sub-Zero bros. were abducted by their father to be taken to China and trained by the Lin Kuei, leaving behind their mother and younger sister in America. The thing is, we never hear of them again, so we don't know of their current status (did they survive Shao Kahn's invasion?). Frost was widely believed to be this long-lost sister of Sub-Zero, but this was disconfirmed by the creators themselves.
Every single comic relief baddie from the Pokemon Mystery Dungeon series games. They all only appear in the very beginning, and they all disappear without a trace as the series progresses. Heck, they don't even return after Primal Dialga has finally been taken care of! It's implied that the main reason why they all disappeared very early is because they are actually all afraid of the series' Big Bad, Darkrai, and that Primal Dialga is the least of their worries.
In Super Mario Sunshine, Bowser Jr. mentions that he got the Paintbrush from "a strange old man in a white coat" as the camera focuses on the E. Gadd logo on F.L.U.D.D.'s side. We never find out if Bowser Jr. stole the Paintbrush from Professor Gadd or if Gadd gave it to Bowser Jr.
It's believed that Gadd invented the paintbrush for Mario to use, and the only reason Bowser Jr. has it is because Gadd gave it to him while he was disguised as Shadow Mario... with Gadd somehow mistaking him for the real Mario.
Then there's Il Piantissimo. The ending of the game shows him finding the Magic Paintbrush, possibly setting up a Sequel Hook. He's never seen again.
Fear Effect. Hana encounters a frightened old woman in a fishing village. She then leaves the old woman behind and the old woman is not seen or heard from again. Really, Hana should have been given a What the Hell, Hero? scolding for that!
One of the numerous subplots brought up in Another Code R is that of Matt's father, who mysteriously disappeared. While all the other subplots and the main plot point are solved, his is dropped in the last two chapters and given only a vague hint as to what happened. The intent was this was going to be a Sequel Hook for a Spin-Off game starring Matt that would answer this question, but became this trope when the company of the series went bankrupt and closed down.
Invoked by Silent Hill and Silent Hill 2 with the fates of Cybil and Angela. Cybil isn't mentioned after the first game (though the only ending where her fate would be in question is Good+; in all the others, she's dead or trapped with Harry), and Angela is never seen again after she acsends the staircase in the second.Word Of God has stated that they wanted their fates to be open to interperetaion.
In Silent Hill Downpour, Murphy goes through the Centennial just to meet up with a DJ named Bobby Ricks, who's been giving dedications to him through the radio for some time. Ricks claims to have a chance of escape, and Anne shows up soon after. Monsters attack, and when the lights come on, Murphy is alone. Anne reappears later and plays a key role, but Ricks is gone for good, though it can be assumed he died; there's something of a blood trail towards the fridge on the studio floor. You might think his body would be in there, but nope.
Soul Calibur 5 really shook up the character list, with almost half the characters from the previous game being removed. Most have retired and passed their skills on to children or successors (Xianghua, Taki), some have just reached the end of their journey and have no reason to continue fighting (Setsuka), some are dealing with their own stuff (all the Korean characters), some are dead or lost in another world (Sophitia and Cassandra) and some have just dropped off the face of the earth. Infamously, Talim and Zasalamel have completely vanished with no explanation as to what happened to them.
In the original version of The Witcher 2 the bastard children of King Foltest simply dissappear with no mention after the Prologue, in spite of their central role to the events. This is somewhat mended in the Enhanced Edition where, if you pick Roche's path for Act 2, you can receive a side mission dealing with their fate in Act 3. Likewise, Letho's minions Serrit and Auckes dissappear from the narration for players choosing Iorveth's path in Act 2.
In the Diablo series, aside from the three Prime Evils (Mephisto, Diablo, Baal), there are the four Lesser Evils. Two of them, Andariel and Duriel, are act bosses (Andariel for Act I, Duriel for Act II) in Diablo II. The other two, Azmodan and Belial, have never actually appeared beyond small mentions in the original game's manual and a fleeting mention in in-game lore.
They finally make appearances in Diablo III, as the bosses of Acts II (Belial) and III (Azmodan).
In I am Alive, Henry's wheelchair is found near the end, but the character is not seen again. The Hero mentions an intention to find Henry, but it is also implied that the character has already been killed. Either way, the epilogue makes no mention of the character's fate.
Also, the helicopter and its pilot in the "Strangers" chapter. The hero sees a newly crashed helicopter on top of a building and theorizes that the pilot jumped out before it went down. There is no way to examine the wreckage any closer, there is never any sign of the pilot, and neither the crash or the pilot are ever mentioned again. (In fact, the incident is so strange and unrelated to anything else in the game, it's just shy of being a Big Lipped Alligator Moment.)
Breath Of Fire 2: During the opening sequence, Ryu's father Ganer and sister Yua disappear. Ganer plays a major role in determining which ending you earn. Yua... is never seen again. It's heavily implied that she grew up to become the thief Patty, who kickstarts the main plot, but this is never confirmed, and even if it's the case, that means she was trapped in Dragnier when the gate was sealed and nobody cared.
Mass Effect 2 zig-zagged this trope. In the Tutorial Level, the player learns that a minor character has betrayed an organization that plays a key role in the story, nearly killed the Player Character, and otherwise set off the events of the plot. The traitor is unceremoniously shot dead before the end of the level. No follow up was included in the game, leaving the traitor's act a complete mystery. Finally, the DLC Lair of the Shadow Broker has dossiers on the various characters, and one line in optional character Legion's file reveals the traitor Wilson was a double agent for the the Shadow Broker. During the months between the game's release and the DLC, there was no explanation for any of it.
In Xenosaga, Dr. Sellers' (one of the villains of the series) fate is left unknown. We aren't sure whether or not he survived the Merkabah being absorbed by Able's Ark.
Arguably with how the series likely will never be finished, the entire plot falls under more of a "What happened to the everything?"
In the Subspace Emissary mode in Super Smash Bros. Brawl, what happens to Link's fairy companion? It appears flying along with him when he's introduced, flies off out of shot when the Halbird casts a shadow... and then (outside of one of the battle taunts Link can do) never appears again.
In Chapter 16 of Ghost Trick, Sissel has to prevent a torpedo that a mouse is perched in from detonating. After Sissel does so and moves on, we never find out what happened to the mouse. A literal example of this trope.