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 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 Manfred 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 fouth 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.
In the "Turnabout Revolution" case of Phoenix Wright: Ace Attorney Spirit of Justice, one of the royal guardsman is sent to bring Phoenix and Miles Edgeworth to see the queen. Usually such minor characters are not given names or sprites, but this one has (he's called Lah'kee). Under the Law of Conservation of Detail one would expect he has something to do with the case, but not only is he uninvolved, he never shows up again after that one scene.
Davis disappears after Salvation. Given he spent that mission's opening cutscene panicking over having contracted the Creeper, though, it's easy to guess what happened to him.
Captain Waylon 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 General Forsythe. 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.
Tabitha's fate is also left ambiguous following the end of Lab Rats. Penny can feel everything the rest of her family feels, so she knows that Cyrus and Caulder are dead without being told, but even she doesn't know what happened to Tabitha.
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.
ANNO: Mutationem: After retrieving Ryan's stolen ROM, Ann discovers he visited Alan Doyle at some point and discovers an underground facility that has ties to The Consortium. Despite traversing through the area, Doyle is never encountered or mentioned again even though he was somewhat working with the Big Bad.
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.
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.
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 he's ever seen again is in the Non Standard Game Over, 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)?
That goes for Grunty's benevolent sister Brentilda as well.
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.
Batman: Arkham Asylum: Zsasz is MIA after you save Dr. Young from him. There's the Scarecrow vision, but that's an illusion. Same thing applies to some of the named staff in Arkham after you save them. Considering how many guards got killed, we can only hope they made a run for it.
Betrayal at Krondor: An intriguing subplot concerning someone calling himself "The Crawler" trying to dislodge the Mockers (i.e. the thieves' guild) from Krondor and set up his own criminal empire crops up a few times in earlier chapters. After Chapter 3, however, it never gets referenced again (other than a brief sidequest at the beginning of Chapter 6). Apparently, Raymond E. Feist thought the subplot was interesting enough on its own to become the basis of the next book in the Riftwar Legacy series: Krondor: The Assassins.
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.
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.
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.
Breath of Fire IV: Ilgor, servant of Prince Morley of Ludia, vanished after his failed attempt to kidnap Ryu to use his power as a bargain chip against the Fou Empire. We do keep running into his underlings in random encounters though, so maybe he never gave up.
The Caligula Effect: The Overdose version adds the Ostinato Musician route, where the protagonist chooses to join the eponymous group. This leads to some altered events, including the fact that Shadow Knife actually survives their fall. But even with them actually still being alive in that route, they are completely absent in Grand Guignol. They only appear in the epilogue scenes for the good ending.
In Call of Duty: Advanced Warfare, Joker and Gideon are tasked with preventing Mitchell and Ilona's escape from New Baghdad. Gideon lets them go and also performs a HeelFace Turn of his own, but Joker is never seen after this mission.
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.
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.
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.
Played with in the third chapter of Danganronpa 2: Goodbye Despair: Both Ibuki Mioda and Hiyoko Saionji are murdered by Mikan Tsumiki, and while both girls' deaths are solved during the class trial, the surviving students are more focused on Ibuki's death than Hiyoko's (Mainly because Ibuki's death has more clues leading to the murderer than Hiyoko's) causing her case to be Out of Focus for most of the trial. What's worse, the murder weapon which was used to kill her (via slashing her throat) is never found during the investigation and no one seems concerned about the fact that they never found it nor does anyone ever bring it up while discussing the incidents.
In Daughter for Dessert, it is never revealed who stole the toaster, or why. Amazingly, its lampshaded by the protagonist at the very end of the story. Mortelli has solved the mystery, but declines to name the culprit.
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 EarthGov 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.
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.
Done In-Universe in Dino Crisis. At the start of the story, Cooper gets separated from the rest of the team and the audience sees him get eaten by the T. rex. The rest of the team never learn of his fate and they don't even talk about him other than how he just disappeared. At the end of the game, Regina mentions in her report that Cooper simply went missing and they haven't heard from him since.
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.
The mage origin of Dragon Age: Origins has a literal example as during your test to prove yourself in the Fade, you encounter another mage named Mouse who wants to help you. As you defeat the lesser demon you were sent to kill, Mouse reveals that he is in fact a pride demon, the most powerful and deadly type of demon. He reveals his true appearance and gives you the ominous warning. "The true dangers of the Fade are preconceptions, careless trust, pride... Keep your wits about you, mage. True tests never end." before vanishing. Despite this disturbing introduction you never see or hear from him again.
There's also the case of Fergus Cousland in Origins. Barring one conversation choice just after the party arrives in Lothering, no mention is made of him at all until the epilogue.
Inquisition also mentions the fates of nearly every party member from the first two games, plus Shale plays a supporting role in the Asunder novel. However, nothing is mentioned of Oghren, Nathaniel, Velanna, or Sigrun from the Awakening expansion. Their absence is especially conspicuous considering the involvement of the Grey Wardens.
Dragon Quest I: The Hero searches for several items scattered around the world by his ancestor Erdrick in Dragon Quest III. He finds his Sword and his Armor, but... Where's Erdrick's Shield (i.e. the Shield of Heroes)? The absence of his helmet was understandable, since it was just an iron mask, but the shield was a special magical talisman like the sword and armor.
Dragon Quest VII: Depending on how diligent you are with talking with NPCs, some plotlines appear to have a few open threads left hanging, like some NPC's fate being left unknown.
Dragon Quest VIII: After his defeat, it is unclear if Sir Leopold is dead or alive as he is not seen again. Signs point to him being dead though — prior to confronting Marcello at Neos, a potential party chat with Angelo will result in him musing over the possibility of having to face and potentially kill his half-brother in battle, taking note of the fact that out of the three sceptre-bearers the party had defeated thus far, two of them ultimately perished at their hands. Since Jessica is very much alive, this seems to point to Leopold being dead after all.
Breaking Veronica's curse and returning her to her proper age beyond a cutscene and a late-game Pep Power with her and Serena — both temporarily — are never brought up or explored.
Unlike the Gloomnivore and Tatsunaga, Avarith is nowhere to be found in the postgame despite not being a Spectral Sentinel and assumedly still being alive.
After learning about Michelle's death, Queen Marina mentions having been trying to find a way to undo the curse of the Mermaid's Burden (where a mermaid who becomes human will turn into sea foam if she ever re-enters the ocean), but it's never brought up again.
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. (You could 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.
The Elder Scrolls franchise, with its open worlds featuring dozens to hundreds of plot-relevant NPCs will obviously raise this question with at least a few of them from game to game. Sometimes, the developers will drop hints to what happened to some of these characters, but a few of their fates remain unknown:
In Daggerfall, Ebonarm is a god of war worshipped in the Iliac Bay region and is held in high regard by the Redguards. He is a Black Knight with an ebony sword fused to his right arm and is never seen without his dark ebony armor. He is a noted adversary to most Daedric Princes and, despite being a god of war, usually appears on the battlefield to prevent bloodshed and reconcile the opposing sides. Ebonarm hasn't been mentioned in any form since Daggerfall, however. He has possibly even Unpersoned in Online, where a book from Daggerfall appears that previously mentioned him, but has all mentions of Ebonarm removed.
The first NPC you meet is Jiub, a fellow prisoner on the Imperial prison ship, who asks you your name and is notable for being one of the few fully voiced NPCs in the game. But after having completed the tutorial, you will never see him again, causing many people to wonder where he went. He was even popular enough to spawn all sorts of Game Mods which add him back into the game in various roles, including as a companion. Bethesda, seeing the fan reaction, got into the act in Oblivion where asking certain characters about rumors will reveal that Jiub has become a saint in Morrowind, because he drove the Cliff Racers out of Morrowind. The Dawnguard DLC for Skyrim fully 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. You can also get a quest from him to collect his scattered memoirs so that his tale may live on.
Another Morrowind character that disappeared was Caius Cosades, the Imperial Spy Master and first major Quest Giver of the main quest. He gets recalled to Cyrodiil part way through the main quest, but is not seen in Oblivion at all, to the disappointment of some fans. 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. (Given that House Hlaalu, Helseth's Great House, was basically Unpersoned following the RedYear, as shown in Skyrim's Dragonborn DLC, maybe this one isn't too unusual after all...)
Vivec, one of the Tribunal deities of the Dunmer who acts as a Supporting Leader toward the end of the main quest, also disappears during the events of the Oblivion Crisis. There are conflicting reports saying that he was taken by the Daedra, was killed by the Nerevarine, or that he escaped into Aetherius (the realm of magic).
In Morrowind you can find light helmets called Colovian Fur Hats, which presumably come from Colovia in the Imperial Province. In Oblivion players can visit Colovia, but there are no Colovian Fur Hats anywhere.
Oblivion's Shivering Isles DLC introduces Jyggalag, the Daedric Prince of Order, Big Bad for the DLC, and the old Sheogorath's Literally Split Personality. Despite being freed and split from Sheogorath, he does not appear anywhere after said DLC. There is no mention of him anywhere in Skyrim (where all 16 other Daedric Princes make an appearance) or any lore piece set in between the two works. Speculations about his fate are a staple in the Elder Scrolls lore community.
Barenziah, Queen and later Queen Mother (to the aforementioned Helseth) of Morrowind is a prominent figure in the series ranging from the time of Tiber Septim in the backstory to her final appearance in Morrowind's Tribunal expansion. She was known to still be alive at the end of the 3rd Era, but what happened to her after that is unknown. Skyrim, set in 4E 201, has some references to her made in the past tense, implying that she died.
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.
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.
Quite famously within the fandom, in Fallout 2 you never do rescue Sulik's sister Kurisu, find Sulik's village, or any trace of the slaver group that kidnapped her as they were all Dummied Out from the final version. Kurisu was planned to appear as a companion in the cancelled Fallout: Van Buren, but she's yet to appear in a game since. The fan-made restoration mod finally lets you save her.
A possible fate of Follows-Chalk in Fallout: New Vegas if you convince him to leave tribal life to see civilization for himself. If you do he's said to leave his tribe at Dead Horse Point and never be seen again.
In Fallout 4, if you convinced Madison Li to defect from the Institute to the Brotherhood of Steel, then later turn on the BOS, she seemingly vanishes from the game, never to be seen again. Subverted in that she is still present in the game world: use of the GECK editor reveals that after the Prydwyn crashes, Li winds up trapped in a room under the rubble of the Boston Airport, still alive but unable to ever escape.
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.
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!
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.
What happened to the people of Narshe in the World of Ruin? There is an NPC that mentions that the town is overrun by monsters, but why? The city looks exactly the same as it did in the World of Balance so it wasn't hit by the Light of Judgement. Did the people die? If so, how? Why did Umaro and Mog survive? Did the people evacuate? If so, where? Considering how important the town is to the story, you would think something would have been said.
In Final Fantasy VII there's a Quirky Miniboss Squad called "The Turks" and consisting of mercenaries hired by Shinra named Reno, Rude, and Tseng who antagonize you throughout the game, and each time they're defeated they run away. During your second and final visit to Midgar, you fight them one last time, and at the end of the battle they run away as per usual. However, not long after the Shinra corporation is completely destroyed with its leadership either dead at the hands of Diamond Weapon or defected. Once that happens, the only thing left to do in the main story is head to the Northern Crater to kill Sephiroth. What happened to Reno, Rude, and Tseng during all this is left ambiguous.
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. Likewise, Prince Puck only makes a few appearances in the first quarter of the game and completely vanishes thereafter until the ending, serving little purpose beyond befriending Vivi. Bonus points for their race being anthropomorphic rats.
Ba'Gamnan in Final Fantasy XII is introduced as a ruthless bounty hunter with an agenda against Balthier. The only thing he does is kidnap Penelo and chase the party through the mines and completely disappears from the story afterwards without any mention of him or his crew ever again. There is an optional boss fight against him via hunts, but unless the player actively completes hunts as they come along, it's possible to never fight him at all or even remember who he is. His appearance in Final Fantasy XII: Revenant Wings can surprise many people who had not fought him in his optional encounter in the previous game.
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.
The school children in the prologue of Final Fantasy Tactics Advance simply disappear when the town is transformed. The three bullies that picked on Mewt are later revealed to have become zombies (and then vampires in a post game side quest), but nothing is ever mentioned of them. The children are shown again in the ending alive and well.
In Fire Emblem: Three Houses, depending on the route you pick, some characters will no-show in Part II and their fates are left unresolved.
On all routes, Marianne makes no appearances in Part II if you don't recruit her.
On the Crimson Flower route, Lorenz and Raphael make no appearances if you don't recruit them. Lorenz's family sides with the Empire in the other routes, so it's likely he's fighting for you offscreen.
On the Verdant Wind route, Gilbert and non-recruited Annette make no post-Time Skip appearances. If you did recruit Annette, it's at least mentioned that Gilbert was last seen at Gronder taking away Dimitri's dead body.
On the Silver Snow route, Sylvain, Ingrid, Felix, Mercedes, Annette, Hilda, Ignatz, Raphael, Leonie, and Lysithea make no appearances.
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.
In Fredbear and Friends, Ashley just sort of disappears when the attacks start happening. While it's likely she's been killed just like Chris and Richard, we get to see the former's Vertical Kidnapping and hear the latter's Sound-Only Death, but nothing as to how she went out. The game lampshades it when Thomas asks the cops what happened to her, only to get no response.
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, which takes place in a different timeline.
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.
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.
Granblue Fantasy: While the main characters have returned to Nalhegrande in the third arc, Pholia, Bai Ze, Baragona, Hal, and Alliah have not been seen in story since the second arc. Pholia and Bai Ze have their whereabouts explained in their gacha fate episodes, but the other 3 have not been mentioned since then.
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.
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. The same could be said about Drs. Gina Cross and Colette Green in Half-Life: Decay. Which is weird considering that Blue Shift was made by Gearbox and its character Barney Calhoun survives the Black Mesa incidence and the ensuing chaos and returns in Half-Life 2 and its two Episodes.
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. (Given what happens to Reach, is that really surprising?) 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 the book takes place right after he leaves to escort Dr. Halsey, one of First Strike's main characters. Eventually, Halo: Initiation revealed that Jun did in fact manage to escape Reach.
Grace in Heavy Rain only makes a few appearances. She's prominent in the prologue where she witnesses the death of her son, Jason, but after the Time Skip, she simply vanishes from the story and is never mentioned until she appears in the police station confront Ethan over the disappearance of their second son, Shaun. Grace does make one more appearance where she tells the police that she thinks Ethan is the Origami Killer, but she then disappears entirely for the rest of the story and is never mentioned again unless you get the ending where she and Ethan reconcile.
Hidden City would frequently introduce new characters for the monthly events, each with unique designs, motives and relationship with the recurring cast. Once the event ends, the characters disappear with it. Occasionally, the game does provide a justification why the character will no longer be appearing (e.g. they left the city); but most of the time, there is no mention that they've left, and the character just stops appearing without reason. One example is Agent Jones, who develops an intense rivalry with the Detective (who is a core member of the cast) but then disappears without a trace and the Detective never even mentions him again.
At the very beginning of Homefront, 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.
While Jacket from Hotline Miami and the protagonists of Hotline Miami 2: Wrong Number have very clear fates that is, dying by nuclear blasts in either Hawaii or Miami if they were not killed at the end of their storylines, the fate of the other protagonist of the first game Biker was not revealed, though it is likely he survived, due to hiding out in the desert rather than staying in Miami.
It's also never revealed what happened to the Technician that the Biker interrogated in the first game. He could have flown away from Miami (meaning that he may still be alive) or, the more likely option, he was silenced by 50 Blessings for giving in and revealing classified information.
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.)
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.
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.
Iron Helix: The opening cutscene shows that the Jeremiah Obrian was traveling with another Cerberus-class ship, the John Paul Jones, however, this other ship is never mentioned again after the opening cutscene.
In Katawa Shoujo, Kenji is all over this trope. Who's his ex-girlfriend? What was in that box? Did Yuuko ever find out he was stealing books from the library? It's all a Riddle for the Ages...His ex-girlfriend is heavily implied to be Yuuko but it's never confirmed. In fact, the prototype build all but shouts it to the player, but that's not exactly canon. Probably for the better that it was made more subtle.
In Kingdom Hearts, Riku warns Sora that "we may never see our parents again" if they leave the islands. This is the first and last time their parents are mentioned in the entire series.
Kairi's grandmother appears in Kingdom Hearts: Birth by Sleep and in a brief flashback (of the very same scene) in the original Kingdom Hearts, but is never mentioned again.
Kingdom Hearts II: Scar is one of two entities in the entire series to retain his body after falling to darkness and becoming a Heartless. The other one is the series Big Bad. This is an amazing amount of willpower, and it's been firmly established that when a person with sufficient willpower becomes a Heartless, a Nobody is also created. However, there has been no hint of any kind that Scar's hypothetical Nobody will even exist, much less become plot-relevant.
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.
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?
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.
The Legend of Heroes: Trails of Cold Steel: Scarlet is nowhere to be seen in Cold Steel III despite being defeated and rescued by Rean, only getting a single brief mention, and it's not known what happened to her after Cold Steel II. In Cold Steel IV, while she doesn't appear in person, one of Crow's bonding events reveals she went back to the Gralsritter, and is now working under Wazy.
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.
The Legend of Zelda: Breath of the Wild has supporting characters from each tribe that help you board a Divine Beast (Teba, Sidon, Ruu, and Yunobo). They are shown to be doing well if you check up on them after clearing a Divine Beast, but they aren't heard from again afterwards and they don't even appear in the finale and the credits. You can also wind up invoking the trope on accident or on purpose if you decide to go to the Final Boss without resolving the problems plaguing the people of Hyrule; sure, you saved the world, but what ever happened to the people and events you skipped over?
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!
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.
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 whose 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.
All of the previous (and surviving) Normandy crew can be met in some capacity in 3 except for one — Rupert Gardner, the Normandy SR-2's cook/handyman, who the game just appears to forget about (unless he died, meaning his name is on the memorial wall).
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.
Medal of Honor: Vanguard has Lieutenant McCollum, the leader of Keegan's platoon, who disappears after the end of the first section in Predators when he orders Sergeant Keegan and his squad to clear Grave of the German forces within.
Sigma's "partner" who is mentioned only once in Mega Man X5, 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, foreshadowed by how Sigma's final battle body is almost identical in design to Gamma from Mega Man 3.
And also the fate of Dynamo from the same game. He shows up two times to fight X and Zero, once after defeating two Mavericks needed to obtain parts for the Enigma, and the second time after defeating two Mavericks needed to obtain parts for the Space Shuttle to destroy Eurasia. After those two battles, however, Dynamo doesn't die, and just disappears from the plot, not showing up as a sub-boss in the Zero Space stages, and nobody even mentions him again. Even though Dynamo shows up in in the next game, he only does so as a Bonus Boss in the alternate pathways after defeating all 8 Mavericks, defeating High Max or collecting 3000 Nightmare Souls. And he doesn't die at the end of the battle either, just teleports out as soon as X or Zero defeat him. None of the games that followed X6 explained Dynamo's fate.
Dr. Cain mysteriously drops off the face of the Earth after Mega Man X3. Mega Man: Maverick Hunter X eventually addresses this by retconning the story so that he's killed by Sigma prior to the start of the first game.
Douglas similarly disappears without fanfare in-between Mega Man X6 and Mega Man X7. The Lifesaver robots also only appear in X5 and are never mentioned again.
The fate of a large number of characters in-between the X and Zero series have also never been revealed. Not just Axl, Layer and Palette (who are understandable since they were introduced towards the end of the Zero series,) but also Alia and Signas.
In the backstory for Metal Gear Solid, Solid Snake has taken up dog sledding in his retirement, and owns "fifty huskies" which he calls his family. Many a dog lover has been made very upset by the absence of dogs in every later game — they are not even mentioned in Metal Gear Solid 2, and in Metal Gear Solid 4 he has three pet chickens but no dogs. Where did they end up? Are they OK? (Some speculate that the dogs in Metal Gear Solid 4 are the descendants of Snake's huskies, explaining their affection for him, but it's not clear why Snake would dump his 'family' on a nuclear disposal cleanup facility on a remote Alaskan island. It's more likely they are the remnants/descendants of Sniper Wolf's wolfpack, as it's implied that one of them is Sniper Wolf reincarnated.) Given that Campbell's response to the line about the huskies is "Don't worry about your dogs"...
In Metal Gear Solid, there's a significant scene after Wolf's death where Otacon begs Snake "what are we fighting for?" and Snake responds, "if we make it out of this, I'll tell you". Snake never tells Otacon what he's fighting for (even in his big speech in the ending) and it never comes up in any of the later games. The Metal Gear Solid 4 novelisation allows Snake to answer the question during a part that, in the game, is a gameplay sequence.
Even if we never hear Snake tell Otacon this in the games, Raiden asks Snake something similar in Metal Gear Solid 2: Sons of Liberty and the rest of the game has Snake discussing in-depth about what kinds of things are worth fighting for. Seeing how Otacon seems just as resolved as Snake in the game, we can assume he received a similar lecture in between the previous game and this one.
Lampshaded 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.)
In the "Spooktacular Spectacular" mission, Tamara mentions that her tail hurts and considers medicating herself with some remedy she has in her lab. We never find out what was causing the pain, or if she used the remedy.
In the song "Big Bad Bill is a Woolly Blue Hoodoo", Buster, Snuffy, and several of their pets are searching the jungle to find their friends, who have inexplicably disappeared. They instead find Big Bad Bill, who invites them to a party, and the friends are apparently forgotten about (provided that the events weren't All Just a Dream or a magical hallucination, which the singer himself isn't sure about).
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.
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 since the ending shows him alive and well while talking to Shinnok.
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.
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?
At one point you meet two random robbers who don't seem to be afraid of all the biomechanical monstrosities roaming around. They stand out because, other than your party members and enemy soldiers near the end, they are the only non-mutated humans you meet. Your team scolds them, takes their loot (a journal) 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.
Parasite Eve has Police Chief Baker, who plays a small role in the story and steps up to protect Daniel's son from monsters on day 3. It's presumed that Baker stepped down to recover from his injuries, but he's never seen or brought up again for the rest of the game.
Parasite Eve 2 has Aya make a brief mention of Daniel from the first game, but unless you know how to trigger that particular line of thought, you'd never learn about what happened to him. Likewise, none of the supporting police officers that Aya worked with previously are ever mentioned.
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 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.
In Peter Jackson's King Kong, Preston takes shelter in a small cave during the first V-Rex attack in which Lumpy is killed. Preston is never seen or mentioned again, and is the only member of the expedition who is neither shown being killed or being rescued.
Pikmin (2001): The 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. 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.
White and purple pikmin were also no shows in Pikmin 3's main story (though they do appear in mission mode and bingo battle), instead being functionally replaced by the flying and rock pikmin. The fate of the white and purple pikmin remains ambiguous at best.
Every single comic relief baddie. 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.
Blue's Raticate mysteriously disappears after the third/fourth battle.
After getting your first Pokémon in Red/Blue, your first task is to retrieve a package for Prof. Oak, who says that it's a specially-made Pokéball. This seems to imply that it's the Master Ball, but you end up getting that from the Silph president instead; Oak's special delivery never gets an explanation. In Gold/Silver, you end up getting the Master Ball from the new region's professor after beating the Elite Four, so it seems likely that this was the original plan for the first-gen games.
In both the original games and their remakes FireRed and LeafGreen, the "Pokemaniac"/"Pokemon Fanatic" Bill accidentally fuses with a Pokemon due to an experiment gone wrong and the player has to help him split from it. While Bill emerges from the machine, the Pokemon he fused with is nowhere to be found. In Pokémon Let's Go, Pikachu! and Let's Go, Eevee!, this is rectified by showing the Pokemon (depicted here as a Nidorino) running out of the machine unharmed right before Bill himself emerges from it.
Pokémon Black 2 and White 2: The Seven Sages zig-zag this trope somewhat; Ghetsis maintains his role as the Big Bad, Rood has undergone a HeelFace Turn and is the figurehead leader of Old Team Plasma, Zinzolin still works with Ghetsis, and Gorm makes a cameo in the post-game. Giallo, Ryoku, and Bronius are not seen at all.
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.
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.
Psychonauts: After collecting all the things you need in order to ride the elevator, Crispin is chased off by Fred and is never seen again. It is unknown if he was still in the asylum after it got destroyed.
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
In Quern - Undying Thoughts, Gamana never says what happened to her friends Rhoren and Tiador after their people, the Dulmar, were wiped out by civil war.
Depending on who you choose to play as in Resident Evil, the fate of Barry or Rebecca won't be revealed. As Chris, the last you hear of Barry is the opening narration that states they don't know where he is, and Rebecca is never even alluded to in Jill's scenario.
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.
In the remake of Resident Evil for Nintendo Gamecube, you find a unique corpse slumped against the wall in the stairwell (where there are later crows on the lights). You can examine it 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 to.
In Robopon 2, W-King and Lisa lampshade their unimportance to the story and disappearance from the plot.
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.
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 protagonist of Shockwave is unaccounted for in Shockwave 2. It's likely he didn't survive the Time Skip.
The Shrek 2 game introduces a new character called Lil' Red, who tags along with Shrek, Fiona and Donkey on their trip to Far Far Away. She appears in multiple levels throughout the story as a playable character, but abruptly vanishes after the Prison Break level and doesn't appear or get acknowledged during the ending.
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.
James himself in Silent Hill 2. The game has no canon ending and the only thing that we know for sure is that he went to Silent Hill and never returned. Later games just makes passing mention to his current whereabouts i.e Douglas Cartman from Silent Hill 3 saying that he was once involved in a missing person case in the Silent Hill and James' father Frank saying that he hasn't hear anything about his son since his trip to the cursed town in Silent Hill 4: The Room.
SLAMMED!: Griss/Giana vanishes from the story after they help betray you.
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.
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.
Early in SOMA, the player has the option to contact Omicron Station via radio. If they choose to do so, someone will answer, and advise them to commit suicide, as "there's nothing left to live for". Later, when the player passes through Omicron, they'll discover that all of the personnel have died via head-explosions, supposedly a long time before the game's events, and no trace or mention of the man that answered the call is ever given or found.
Sonic the Hedgehog: In Sonic 3 & Knuckles, if you got all the Chaos Emeralds (from the Sonic 3 part) you could, in addition to turning into Super Sonic, start upgrading them into the larger "Super Emeralds" in the Sonic & Knuckles part, allowing you to become Hyper Sonic, who was like Super Sonic only even more powerful. After this one appearance, the Emeralds are only seen in their standard small form, with no mention of the Super Emeralds or Hyper Sonic, although Sonic Mania referenced the former by having powerless stone replicas take their place in Hidden Palace.
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.
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.
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. Obviously, he survives, given his later game appearances, but how he got back is the real question.
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.
The ending of the game if you didn't get 100% shows Il Piantissimo finding the Magic Paintbrush, possibly setting up a Sequel Hook. He's never seen again, and Bowser Jr. has the paintbrush back in all subsequent games.
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.
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.
In the world of Team Fortress 2, the main company providing the mercenaries with their weapons and gadgets was supposed to be TF Industries, and Mann Co. was merely introduced as a division of it. Except TF Industries seemingly faded out of existence while the story immediately began to revolve around Saxton Hale, Mann Co. and the Mann family instead by the time the game got it first Halloween update.
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 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.
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.
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.
In Terranigma, nothing is said about what happened to the characters of Meilin, Meihou, Perel, Fyda, and Roy after the events on Beruga's airship. The airship ends up crashing in Australia, so it's likely to assume that they all died in the resulting crash, but Ark doesn't even spare a single thought about the airship anymore. Though one could think that, since he's heading back to the Underworld for the final confrontation, he probably had other things on his mind.
At the end of There Is No Game, everything disappears except the narrator. We never find out where they went or if they're still around.
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?)
The Tomb Raider series features a few examples. In The Angel of Darkness, Gunderson, the big brute, is sent to contain the situation involving the proto-Nephilim. He is never seen or mentioned again. This is quite jarring, because he was one of the members of Eckhardt's Cabal. Also, Jean-Yves in Tomb Raider: The Last Revelation is shown to be one of Lara's few friends she can rely upon when she needs assistance. Werner von Croy later kidnaps him and Lara does save him near the end of the game, but he vanishes from the story entirely and is never mentioned again. He is also ignored entirely in the later sequels due to the real life Jean-Yves threatening to sue Eidos for using his name and likeness without his permission.
Utawarerumono: 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.
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.
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 is... And despite the long, involved history in the diary that seems to indicate that their problems are intrinsic to the game.
What happened to Chet or Andre (depending on your choices) after they leave Herschel's farm?
What happened to Lilly after the group abandoned her/she abandoned the group? You find out when she returns in Season 4, worse than ever, as the Big Bad and leader of The Delta.
What happens to Molly after she leaves the group?
What became of the Save-Lot bandits?
Or the surviving members of the St. Johns family, if you choose not to kill them?
What happens to Christa after Clementine runs away in the first chapter of Season 2?
Or the guys who were attacking them, for that matter?
Where do Mike, Bonnie and Arvo go after they shoot Clementine and flee the group?
Averted with the cancer survivor group in Season 1, who steal the boat Lee and Kenny had been hoping to use to escape. Their fates are revealed in 400 Days.
However, it is Played Straight at that point, because we don't see them again after Shel and Becca leave them
Speaking of 400 Days, we also don't find out what happened to Leland, Wyatt's friend Eddie, Nate or whichever prisoner escapes with Vince
The survivors from 400 Days who you helped get to the Howe's department store? Are they killed when it is overrun by zombies in Season 2? And if so, doesn't that make "saving" them pointless?
We don't know if Edith, the woman from the "Wellington" ending for season two who appears in flashbacks in season three survived the bandit raid or not. We also don't know what happened to Kenny in that ending.
Depending on the player's choice, either Joan or Clint will die, while the other will flee. Whoever managed to escape, their status will be marked as "unknown" on the choices summary at the end of the season.
Season four reveals that Richmond was attacked, and Clementine can't return there. Javier and Kate, Gabe, or both, depending on player's past choices, are never heard from again, though Word Of God confirmed that they made it out alive. Conrad can also survive the entire season, but is also never seen again.
If the player chooses to spare Lily, she will escape on a raft from the Delta boat, using the chaos that erupted after the bomb explosion as a distraction. This is the last episode of the series, so we never see her again.
If James wasn't killed by Lily, he will separate from Clem and AJ during episode four. Again, he's never seen again, but Word Of God confirms that he lives in the woods near the boarding school and isn't on speaking terms with Clementine.
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 FaceHeel 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.
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.
An 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.
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.
In The Witcher 2, Saskia was a goddamn dragon disguised as a human leading a rather effective peasant revolt. Given that, it's a little weird that she wasn't even mentioned in The Witcher 3 outside of a Gwent card. One assumes that, given the massive scope of Witcher 3 even without Saskia, CD Projekt RED was cutting off some branches.
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 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?"
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 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.