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.
The Dawnguard DLC for Skyrim answers the question: Jiub was soul-trapped and killed by a Dremora during the Siege of Kvatch. How do you know this? Jiub tells you so himself in the Soul Cairn.
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 fate of the Nerevarine, after leaving for Akavir as rumoured in Oblivion. Since they were cured of all the negative effects of Corpus, but retained the positive ones, they should still be alive and well by the time of Skyrim.
...Unless the Nerevarine perished on Akavir. While he is certainly ageless, that does not exempt death. Even worse, lore dictates that the Tsaesci of Akavir had 'ate' the native humans of the past... though the source for that looks very unreliable in light of later revelations on what the main source on Akaviri information was and who were part of the relevant incursion.
In Brave Fencer Musashi Bubbles and Gingerelle, two higher ranked members of the Thirstquencher Army, just utterly and completely vanish about halfway through the game after failing to capture Musashi. A common Fan Wank has it that the Big Bad killed them for their failure afterwards.
The fourth case of Phoenix Wright: Ace Attorney: Trials & 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 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. Another interpretation is that the thief lost the diamond when she tried to escape via a river which she vastly underestimated the danger of.
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. The creators have 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.
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.
In case 2-4, Matt Engarde's cat, Shoe, only serves as a one-two plot device (while talking to Maya's kidnapper, Phoenix hears him meowing in the background, revealing that the kidnapper is at Engarde's mansion), and is never mentioned again afterwards in the game. A promotional artwork shows that Gumshoe adopted Shoe, along with Polly the parrot.
The fate of the character Schala is unexplained/occurs off-camera. This character's fate was most likely planned from the get-go, however, as the second and third games, Radical Dreamers and Chrono Cross, explain what happened to them. However, while both games' explanations have similarities, they are radically different:
In Chrono Cross, Schala ended up in the Darkness Beyond Time, where she remained until Crono and his friends kicked Lavos's ass. After that, Lavos was sent to the Darkness Beyond Time as well, where it found and absorbed the young princess, slowly corrupting her mind and turning their fusion into the Time Devourer. Despite her best efforts to stay conscious, Schala couldn't resist for long, and created a clone of her with the last of her power. That clone manifested in 1,000 AD as the baby girl Lucca found at the end of Chrono Trigger. Only when Serge came and defeated the Time Devourer using the Chrono Cross was Schala freed at last. This fate is considered as the canon one, but an easter egg suggests that the events of Radical Dreamers happened in another dimension.
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 it can be assumed that the Happy Mask salesman helped him get home. But Navi is never mentioned again (or at least not till her cursor cameo in Twilight Princess for the Wii).
The Legend of Zelda: Ocarina of Time had quite a few examples of this after the seven-year time skip. The sudden disappearance of the Happy Mask salesman and his shop is an obvious one. But there are others, too, such as that kid who liked to play in Dampé's graveyard (his home was, strangely enough, where the Bazaar was relocated after Hyrule Castle Town was destroyed by Ganon). It's probably fair to assume that they left the kingdom of Hyrule during this time (and that the developers needed to conserve memory on the 256 meg cart), but the sudden unexplained absence of these characters is pretty jarring nonetheless.
And then there's The Legend of Zelda: Link's Awakening, which ends with Link waking up in the middle of the ocean amid the wreckage of his boat, with the Wind Fish flying overhead. It's never stated if he ever managed to return to Hyrule — Hyrule Historia even notes that he was never seen again after this. A common fan theory is that the presence of seagulls overhead implies Link woke up relatively close to land, though this doesn't resolve the matter of where he ended up, and what occurred after that.
Sigma's "partner" who is mentioned only once in Megaman X 5, but played a key role by building Sigma's body, apparently used to be an old comrade of X, and hates him just as much as Sigma. Since the plot was run off the rails in later installments by Executive Meddling, this partner is never so much as referenced ever again. According to Word of God, had he had his way it would have been Dr. Wily in some form or another.
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 Pińata 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 is... 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 G-Man, 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.
In the Dead Space series, the fate of Lexine Murdoch, one of the protagonists of Dead Space: Extraction and Dead Space: Severed, as well as the origin for her immunity to the Markers' signal, remain unknown. We find out that Lexine is immune to the Marker on Aegis VII during the course of Extraction, when Gabe Weller notices that she doesn't witness any hallucination, one of the many effect of the Marker, while everybody on the Ishimura did to some extent, Gabe included.
In Dead Space: Severed, we learn that Lexine's immunity is now at the center of a scientific project called the Oracle Project. This project, whose goal was to wait for Lexine to give birth to a child and to study the effect of the immunity on him - presumably to spot a gene responsible for it -, is eventually scrapped when the outbreak on Titan occurs and Lexine's termination is ordered. At the end of Severed, Lexine flees to an unknown location (presumably Earth) with the help of Gabe's sacrifice. Her status in an Earth Gov file shown after the credits indicates that she is still alive, missing and a target of the Earth government. She's never heard of after that, neither in the sequel or in any of its DLC.
Given the ending of the series and the fate of Earth and Humanity (and possibly all organic life) at the end of Dead Space: Awakened, it can be safely assumed that she suffered the same fate as everyone else. Not that her immunity would have been helpful in any way to keep that, or even the whole plot of Dead Space 3, from happening.
The Final Fantasy series has notoriously bad continuity as far as sidequests go.
Banon 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 was killed after the Empire's fake surrender, but this is never confirmed and none of the party (which includes Banon's long-time friends, Edgar and Locke) even see fit to mention his apparent death after Edgar leads the currently inactive portion of your party in a narrow (offscreen) escape to reunite with Locke's portion of the group. Likewise for Banon's right-hand man Arvis, also a long-time friend of Edgar and Locke. Were Banon and Arvis killed before Edgar uncovered the Empire's deception, or did they perhaps lead La Résistance's nameless infantry in a Heroic Sacrifice to buy time for Edgar's getaway? We'll never know, because even almost 20 years after the fact, the creators refuse to say.
Siegfried 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? Nope. It later comes out that the goofball you met on the Phantom Train was an impostor impersonating a legendary warrior, but that only raises further questions that never receive answers.
After Kefka poisons the people of Doma, the only survivors are Cyan and a nameless soldier, who search the castle for other survivors. Cyan finds his deceased wife and son and goes on a Roaring Rampage of Revenge, hooks up with Sabin, and the rest is history. Whatever happened to the other survivor? The Imperials did not occupy Doma Castle (Kefka poisoned the water on his own, rather than being ordered to do so), so it's not inconceivable that he might have survived the siege, but he's never heard from again.
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. Bonus points for their race being anthropomorphic rats.
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.
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.
The remake of Resident Evil for Nintendo Gamecube has a minor example. In the stairwell (where there are later crows on the lights) you find a unique corpse slumped against the wall, who can be examined to read "What the hell happened in this mansion?" Later on the corpse is just... gone, you never encounter a zombie that looks like it, and nobody knows where it wandered off too.
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 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...
One was also very narrowly averted thanks to a Hand Wave in Golden Sun 2. Remember Babi, the old man who's life was a major plot point in the first game, and who needed you to go to Lemuria to prolong his life? Yep, he died. That's it. You hear just once in an offhand comment that he died, and nothing more is ever said about him at any other part of the game.
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.
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 WoW 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).
Even the playable Draenei have been largely sidelined. At one point, they weren't invited to a major Alliance meeting because the member calling it forgot about them.
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.
Medivh intentionally does this, disappearing off the face of the earth with no explanation beyond him feeling it wasn't his time anymore. That said, he had been used by a demon god to cause some of the worst wars in history, so he can be forgiven for wanting to step out of the limelight.
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.
Grand Theft Auto V has a few. For example, several missions involve Michael opposing his daughter's involvement in a talent show. He finally relents, but unless you happen to know to tune into the in-game radio at the right time, or find the right in-game Internet posting, you may never find out if she won or not.
Depending on the ending that you choose there are many.
If you choose to kill Trevor, the game ends without ever resolving problems with Devon Weston who owes Franklin money and wants Michael dead.
If you choose to kill Michael, the game ends without ever tying up Trevor's story - both Wei Cheng's Triads and the FIB want him dead but we never hear from them again.
Both endings in which you choose to kill one of the main characters fail to resolve Franklin's plot line; Stretch is still alive and does not get any sort of retribution for betraying Lamar and Franklin.
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 is deliberately keeping her fate a secret for dramatic effect doesn't help.
The reason Asuka is in Tekken 5 is to be a replacement 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 his ending. 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 onward, (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. For that matter what happen to the first Kuma?
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 Colons. Their kidnapping is a major motivation for their adoptive mother, Curly—until the Core fight, after which Curly never mentions them again.note 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 Colons 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 one of the consequences of half the game being Dummied Out because of space constraints and 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. 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 happens 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 VI... five games and 16 years after his first appearance.
What happened to Dogi during V? Or during Memories of Celceta (which takes place between II and The Oath in Felghana), for that matter. Flashbacks in the latter show him in Celceta with Adol (albeit unnamed), but he never makes an official appearance.
In Lufia II: Rise of the Sinistrals, Maxim's childhood friend Tia. She's your second party member and obviously is in love with Maxim and the game seems to imply a Love Triangle beginning between her, Maxim and Selan. As Rise of the Sinistrals is a prequel to Forest Of Doom, it's obvious that Maxim and Selan will end up together and Tia leaves the party, and game, when the two get married. She doesn't even return to her item shop from the beginning anymore, completely gone until a small scene during the credits.
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, 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-infested 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 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 Face 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, the fate of Jun from Reach was left ambiguous; he didn't even get a mention in the 2010 reprint of Halo: First Strike, despite the fact that takes place right after he leaves to escort Dr. Halsey, one of that book's main characters. Eventually, Halo: Initiation revealed that he did in fact manage to escape Reach.
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?)
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.
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 Goombella'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.
It could be thought that they will return when the planet really is overcome by tiberium, since tricking them into thinking that was the case was what caused them to arrive in the first place. However, with the later development of control over the crystal growth, such a fate might be averted.
The Legend of Dragoon reveals in the third disc Shana is the twin sister of the dead Princess Louvia, which makes her daughter of Queen Theresa 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. SOLVED! Cyrax and Sektor both feature in the Mortal Kombat X comic, in which Cyrax regains his humanity, Sektor is killed by the reborn Sub Zero, and then Cyrax sets his self destruct to blow up the Cyber Ninja base. So they both are and aren't dead. That's what happens when you choose to set your game after a 25 year time skip. Shit gets missed!
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 Pokémon 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.
Subverted with Gengar on the first two games. Even though he's seemingly the leader of your average Goldfish Poop Gang, he turns out to be far worse when he tells everyone in Pokemon Square that you're the cause of The End of the World as We Know It. His gang is almost never seen again with him, but they stay as recurring characters. However, their original plan about taking over the world has this trope played completely straight.
In Red/Blue, your very first mission and storyline dungeon requires saving a Caterpie and returning it to her mother. The Butterfree is then completely erased from existence as she is never seen again. Strangely enough, Caterpie DOES gets a role as a supporting character.
Also, in the first generation (main series) and their remakes, Blue's Raticate mysteriously disappears after the third/fourth battle. Due to the fact that this is seen in Pokémon Tower, it has led many fans to believe that Red (the player) accidentally killed it (although this is very unlikely).
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., especially because E. Gadd never makes a physical appearance.
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 ascends the staircase in the second.Word of God has stated that they wanted their fates to be open to interpretation.
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.
Soulcalibur V 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 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 Diablo II, Natalya the Assassin stays in Kurast, and leaves after Mephisto is defeated, with no explanation. In Diablo III, the Natalya's Vengeance item set vaguely describes her leaving assassination to become a Demon Hunter.
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 II: 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.
Patty's fate, at very least, was finally answered in the GBA port of the game. With a still image, during the end credits, showing her gazing at the horizon, in what looks like to be on top of the hills where the sealed gate to Dragnier is.
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 Lair of the Shadow Broker DLC 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 Shadow Broker. During the months between the game's release and the DLC, there was no explanation for any of it.
Speculation that Dark Energy was causiing Haestrom's star, Dholen, to prematurely enter into the Red Giant phase was heavily hinted as being an important future plot point. In the third game however, it was not mentioned at all, making this apparently an Aborted Arc.
Not only that, but the two characters who's final scenes in 2 implied they were going to look into the Dark Energy thing, Gianna Parasini, and Kal'Reegar, don't appear in the 3rd game at all, despite nearly everyone else surviving from both prior games making an appearance. Reegar is mentioned in a report to have died in battle, while Gianna is not mentioned at all.
The original plan was to have the third game reveal that the ubiquitous use of mass effect technology has a dangerous side effect, and what is happening with Haestrom's star is only the beginning. The Reapers would have been revealed as preventing the stars from being destroyed by the misuse of the technology by destroying races.
Bodahn and Sandal seem to have quietly dropped off the map in Dragon Age: Inquisition, with the role of dwarven enchanter taken on by Dagna, a minor (but adorable) NPC from Origins. Especially frustrating since Sandal was built up to be a very weird mystery—what is he? A dwarven mage? An abomination? A reincarnated Elder God?—and then was seemingly forgotten about.
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 Halberd casts a shadow... and then (outside of one of the battle taunts Link can do) never appears again.
She probably is the same fairy that shows up up if you use his side taunt, implying she's just hiding inside his clothes.
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.
Also, what happened to Dandy and Beauty? The last time we see them, we learned that Beauty could sense Sissel, then we never see them again until the post-game Where Are They Now segment.
In the intro of Mario & Luigi: Dream Team, Broggy (Broque Monsieur's dog from the last game) shows up to deliver the letter to Princess Peach's Castle inviting them to Pi'illo Island. After this however (and the point when the blimp lands), he's never seen again for the rest of the game and isn't even mentioned by anyone.
The first game's best ending has a number of Onions in new colors flying into the planet's low orbit. The sequel drops this, as neither of the two new types of Pikmin have Onions. By the third game, the design of them is altered altogether, and the new Onions never leads to anything aside from serving as a slight Sequel Hook.
The fate of the Purple and White Pikmin in the second game. Unlike the primary types, they live in the Hocotate Ship. That same ship that flies back to Olimar's home planet. What makes matters worse is that they are not seen in the game's true ending at all, the primary colors being the only types to appear.
In Robopon 2, W-King and Lisa lampshade their unimportance to the story and disappearance from the plot.
Final Fantasy Tactics: Due to the game's mechanic, any named characters offering to join Ramza will be Put On The Bus because of the possibilities of the offers being denied, battle deaths, or them getting laid off. While it's shown that Ramza and Alma survive the explosion in the final battle, the rest of the army isn't bothered. Likewise, Final Fantasy Tactics Advance and Final Fantasy Tactics A2 doesn't address generic party members at all and they may as well not exist according to the endings.
Halfway through Avencast: Rise of the Mage the player steps through a Point of No Return. This leaves the handful of survivors to deal with the remaining enemies, despite the fact that if any were capable of doing so they'd have already done it. Worse, the distress call to other academies is never addressed after it is made.
The protagonist of Shockwave is unaccounted for in Shockwave 2. It's likely he didn't survive the Time Skip.
In The Logomancer, Ardus reveals at one point that the ideal Love Interest he created for his novel looks and acts exactly like Cynthia, even though he wrote the manuscript long before he met her. Everyone is quick to point out how weird this is, but it never comes up again.
What becomes of Dee, Anzel, Bill and Trot at the end of Emerald City Confidential? Their storylines never get resolved as the game gradually focuses more on the main plot.
Left 4 Dead 2 has a gun store owner named Whitaker who helps the survivors reach the mall during the Dead Center campaign if they get him a pack of cola. You never get to hear if anything happened to Whitaker once you leave, though it is presumed that he spent the rest of his days holed up in his gun store with whatever food and supplies he had left.
Captain Waylon in Advance Wars: Days Of Ruin just vanishes at the end of Waylon Flies Again. What makes it such an odd example is he sets himself up perfectly for a good dose of Retironyand was the man who offed Captain Brenner, a major character. While it's possible he died during the battle like a few other characters have, you'd think he'd at least get a cutscene or a death rattle.
Antichamber: If you find and activate all of the pink cubes before finishing the game...good for you.
In Alone In The Dark 3, the corrupt sheriff under the Big Bad's orders is last seen at the scene of Carnby's resurrection. While all of the other members of the Quirky Miniboss Squad are killed by the end of the game, the sheriff isn't encountered again.
''Persona has several party members you can choose from for a 5th ally, but whoever you pick, the rest simply go on their own way and are never heard from again. The students and faculty that appear in the beginning of the game literally vanish with their school at the beginning of the game and you never find out what exactly happened to them due to an alternate quest that could not be implemented in time. In the PSP port, you can play the alternate quest proper, but you'll see other characters simply disappear or never show up without any explanation. Despite the fact that you can never recruit every main character, Word of God says everyone worked together.
In Yu-Gi-Oh! Reshef of Destruction, unlike the rest of Pegasus' lackeys, the Puppeteer of Doom is only seen once near the very start of the game. He's neither seen nor mentioned after that.
Mira being absent in Baten Kaitos Origins is explained by it being a Vanishing Village. Hassaleh being mysteriously absent from Baten Kaitos: Eternal Wings and the Lost Ocean is never mentioned, explained, or even referenced.
In Far Cry 4 we have Darpan, one of the founding members of The Golden Path who is captured alongside Ajay in the very beginning of the game by Pagan Min. The last we see Darpan he is strapped to a machine being tortured by De Pleur, and the last we hear about him is a passive mention of him in Durgesh Prison. After that no other character ever mentions him, we never learn if he was killed or merely imprisoned, and the game just sort of forgets about him.
In Telepath Tactics, Doran, Edwin, and Gunther don't get epilogue scenes. Neither does Siripent, though one can presume that his wife Sarn's epilogue applies for him too.
The Witness: Subverted. The people who inhabited the Island beforehand are never brought up over the course of the game — unless you get into the hidden areas of the mountain where it is revealed that the Island is a human-engineered Lotus-Eater Machine, designed to flood the senses with metaphysical thoughts to find the true purpose of existence. The previous inhabitants were the programmers who built the island. But we still don't exactly learn what happened to them either, though the walls of the monastery hint that they all fell victim to the Island in some way.
In Episode 1, the crew encounters a Lesser with an augmented (cybernetic) leg. They note that this should be impossible, as Lesser biology is incompatible with cybernetics, and Lessers shouldn't have the resources anyway. How the augmentation happened is never explained.
In Episode 2, Daszk is mentioned to be part of an Inquiry-like peacekeeping force who left him for dead. They never appear.
Also in Episode 2, Ral at one point says the enigmatic line, "That lacertian agrees with me." We never learn who she was referring to.