When someone dies in a cutscene, because the story gods have demanded it. It doesn't always fit with how the game handles combat death and wounds, be they Non-Lethal K.O. or Only Mostly Dead and it doesn't matter how many extra lives the player has left. Characters who have taken fireballs (and worse) to the face at pointblank range will be felled with a single gunshot or stab wound, even if they're level 99. Don't even try your resurrection magic, it would be wrong. A few games actually see magic users or clerics attempting to heal fallen characters, but failing, somehow implying that the dying character is injured in a way beyond conventional methods of healing to help. It's technically a Hand Wave, but they tried. Another reason this could be is that the spells do not have the power to bring back the dead, they just can revive the unconscious. Sometimes this happens in RTS games as well, where in most levels a death can easily be fixed by building the relevant unit production structure. This is generally because developers found that when players weren't able to build heroes back during campaigns, they'd frequently ignore some of the most powerful units for fear of them dying.
If the killed character is an NPC, it's even worse, the gameplay mechanic usually simply doesn't allow the player to revive such a character.
The flip-side is that, occasionally, what the story gods took away, they may give back; there may be a way to bring someone Back from the Dead in a cutscene, but it's usually optional. If not, well, that's what makes it drama.
Usually a glaring example of gameplay and story segregation. Very commonly part of a Player Punch and Death by Origin Story.
Roughly, this is the worst form of death in video games, going plotline death, Final Death, Only Mostly Dead, and Non-Lethal K.O..
Inevitably, a character who is killed in this way will generate an Urban Legend of Zelda regarding how they can be revived, even if actually reviving them is impossible.
Inverse of Cutscene Power to the Max, where a character does nigh-impossible feats, including defying death, merely by the virtue of being in a cutscene.
This is obviously a death trope. It contains major unmarked spoilers, so read at your own risk.
The difference between Plotline Death and gameplay death shows up again in God of War... But it's the opposite of the usual difference. When Kratos dies in gameplay, it's permanent, and you have to reload the last checkpoint... however, when the plot requires him to die, he's allowed a chance to fight back out of the Underworld and complete his quest.
Given the circumstances of the death (killed by Ares seconds after claiming Pandora's Box, the one weapon that can kill him), and knowing Kratos, it's possible that when he dies in the plot, he's finally pissed off enough to kill his way out of there. That, and it's only on that visit that someone drops a rope for him.
Circumstances of his death is probably the key, especially since it's implied he needs supernatural help to be able to escape from the Underworld. If he dies before claiming Pandora's Box, then he's just like anyone else who tried to get it and failed. If he dies after climbing out of Hades and challenging Ares, then even the power of the Box wasn't enough to kill the God of War.
The same thing happens in Jade Empire. If you die, it's reload time, unless you're killed confronting the Big Bad, since that's where you're supposed to die. You then fight your way back from the afterlife.
Regardless of whom Cole decides to save in Infamous, his girlfriend Trish will still fall to her death. This ends up motivating Cole to try to gain more powers and will not run away from the Beast in the future. In the 2nd game ending, its either the conduits or the humanity lives depending on your Karma.
Throughout the Story Mode of Mortal Kombat 9, whoever has to kick the bucket will do so in a cutscene between fights, ranging from Scorpion immolating the original Sub-Zero at Quan Chi's behest to Shao Kahn snapping Kung Lao's neck] to Sindel single-handedly massacring the Forces of Light before Nightwolf pulls a Heroic Sacrifice.
In Killzone 2, you play as Sev, a soldier with a "medic gun" that can heal downed soldiers (as long as they haven't been shot in the head). Some time near the end of the game, one of your partners, Garza, is wounded by Radec and eventually dies. Why you couldn't use your Medic gun to heal him doesn't make much sense.
The FPS Requiem: Avenging Angel features a Plotline Death that must be reversed to continue the game. (One of the player's powers is "revive")
Also, later in the game, a semi-major ally character dies. It makes sense that you're unable to revive her, as she is blown to pieces, and your revive ability requires an intact body to function properly.
In Clive Barker's Jericho, two of the Jericho Squad members, Devin Ross and Paul Rawlings, have the ability to heal fallen comrades, provided that they maintain visual contact. Close to the beginning of the game, however, Ross dies after being slashed across the chest and dropped from a great height, and, no matter how hard he tries, Rawlings can not bring him back. This is important to the game mechanics during the following levels, however, as Ross' spirit lives on, possessing the bodies of his squadmates, so that he may share their consciousness and use their abilities, as well as still being able to use his own healing abilities.
Also, just before the final boss fight, both Simone Cole and Xavier Jones are killed by the Firstborn, who uses its powerful blasts of lightning from its hands to blow them into bloody chunks. They cannot be revived at all, and no-one even tries, quite possibly because bringing back someone from the dead who has been blown into tiny pieces would be a tad difficult. This is also necessary for the mechanics of the boss fight, as the Firstborn is able to use the squad's magical abilities against them, and it wouldn't have been feasible (or really very fair) for it to use Cole's time-slowing/firepower-increasing abilities or Jones' astral projection against the other characters.
Pretty blatant in Call of Duty, especially the fourth. Non-plot essential characters drop like flies, but if they are plot-essential, then they're invulnerable to damage. Then in some later scene, they die, of course.
Some of the main Player Characters have this happen! You get to play out their final moments in first-person!
This is what happens to Bill in Left 4 Dead 2 in The Passing campaign. Despite the fact that survivors respawn in closets when killed and the sequel introducing the Magical Defibrillator to revive on the spot, Bill is truly dead Was revealed in The Sacrifice comic that he was attacked by 3 Tanks while he tried to get the bridge with his friends up.. Naturally, an Urban Legend of Zelda spawned from this, saying Bill can be brought back to life with the defib. Obviously, it doesn't work.
In Borderlands 2, Roland is killed by Handsome Jack late in the game, immediately after Angel commits suicide with your help.
Rather sloppily handled for at least one event in Terra Nova: Strike Force Centauri. In one mission the PC is captured by the bad guys and some of your buddies show up to bust you out, the "mission", such as it is, being "run to the exit". Schuyler, one of your guys, dies immediately as the mission starts (even though his health is full, no-one has even fired a shot yet, and they apparently managed to sneak in completely undetected - in full power armour no less). Makes even less sense as teammates (other than you) are almost never killed by running out of suit energy; the suit then "evacs" them from the mission when it hits critical (which is exactly what Schuyler does, complete with Casual Danger Dialog) so this is rather jarring. Made worse by the fact that it's not even a particularly hard fight to get to the exit, and you are never really under any threat.
During the epic "While Guthix Sleeps" quest in RunescapeLucien does this to several NPCs, including Hazelmere, who acted as a mentor in earlier quests, and two Slayer Masters, one of whom (Duradel) was the strongest Slayer Master in the game at the time the quest was released.
One of the required quests, Path of Glouphrie, has the player about to be killed in a death trap. Hazelmere, mentioned above, manages to teleport in and use a magic seed to save the day. Before arriving, Hazelmere was having a chat with his god about how he would need that seed to save his own life during While Guthix Sleeps.
Invoked during one of the Dungeoneering sagas. You play as a Forgotten Warrior attacking a group of player spoofs. After beating them in the fight, you forcibly take their Ring of Kinship (in Daemonheim, you need to have one with you to enter and to choose your party), and then kill them. The Forgotten Warrior states that they would simply respawn if they had their rings.
And then the game retcons itself by resetting time to before the games starts ensure that none of the events ever happened. ever.
In Ratchet & Clank Future: A Crack In Time, Ratchet dies in a cutscene after taking a relatively weak looking energy blast to the chest from General Azimuth's wrench. Clank goes back in time later on to save him and succeeds, but one does wonder why Ratchet's nanotech didn't just heal him in the first place...
Fridge Brilliance: He didn't have his armor turned on. The devs game him Holo-armor so that they could turn it off during cutscenes. Due to the fact that he was completely unarmored, the weak looking energy blast offed him.
Otomo in Battle Realms, if you choose to follow the Dragon Clan plotline.
In Rise of Legends Carlini dies in a cutscene near the beginning of third campaign by the god of Death himself, meaning he can't come back at all. Normally it just takes some resources and time to revive a fallen hero. Moreover in this mission you get to control a hero that has ability to resurrect friendly units.
The Warcraft series, including World of Warcraft, is fairly loaded with these. The RTSs vary between having missions fail if critical NPCs die or (in III) simply letting you pay to raise them. In the MMO, it's worse: gameplay-wise, every player and every NPC respawns after being killed, in intervals ranging from a few seconds to a week. This applies even if you personally walk into Thrall's room in Ogrimmar and slaughter him. But if an NPC has to die because a quest says so, or the story has to advance between content patches, well... that's it.
Confusingly enough, however, the spirits that can raise a player from the dead actually do so in canon as well, one featuring in a cataclysm quest.
Sort of subverted in the Tactical-RPG Agarest: Generations of War. Canonically, the lead character of each Generation and the three females chosen by Dyshana die at the end of their Generation e.g. Leonhardt, Fyuria, Luana and Elaine all die at the end of the First Generation. However, it is possible to bring back a "mindless, heartless" Marionette version of these dead characters by obtaining the Forbidden Book items and taking them to the Alchemist's Guild. These Marionettes have no purpose plot-wise; they exist merely for people who wish to use them in battles.
In Final Fantasy VII, Aerith's death is important to the story, so you're not allowed the chance to use a Phoenix Down to bring her back.
In a Plot Armor reversal, in the Kalm "flashback" when young Cloud is running around with Sephiroth, Sephy is near-invincible in random encounters and will revive Cloud if Cloud dies. It gets more bizarre if in the flashback, Sephiroth's AI decides to be a jerk and never revive you. This can lead to a hilarious moment where after Sephiroth is out of Cloud's party, Cloud is running around town by himself in his "dead" state. (And then Sephy dies instantly if you poke him with a straw at the game's end...)
In Final Fantasy V, after Galuf's battle with Exdeath, your other party members attempt to use healing spells and items, including a Phoenix Down, to revive him. It doesn't work, and he dies anyway. (because he was simply too far gone, having single-handedly fought Exdeath even when he was technically dead.)
Played with in Final Fantasy IV: at one point, the party doesn't even get a chance to fight Golbez — two side characters are just blown out of the way in a cut scene. After he leaves, they sure look dead enough, but Rydia enters to revive them. The same game has Tellah burn out his life to cast Meteor in an earlier sequence, putting him beyond resurrection. Before that, two sibling wizards petrify themselves to save the main characters from a room closing in on them. Although you can attempt to use spells to revive them, it is explained that the bond between the wizards is so strong that no magic can break the Break spell. An explanation that falls flat on its face, to say the very least, when the spell does get broken off-screen later in the game. By a wizard explicitly less powerful than Tellah, who tries and fails to break the spell on-screen.
The game is however generally quite fond of Plotline Deaths as a means to make room for new or returning character. However, most of the characters return to life near the end of the game, and the GBA remake allows the player to choose among them for the final dungeon as well as the two bonus dungeons of the remake.
Final Fantasy Tactics usually plays this straight, but one of the sidequests has a cutscene in which Mustadio gets the crap kicked out of him and Ramza starts hollering for a Phoenix Down. Mustadio survives. Now just think, if someone (cough, Ramza, cough, Delita) had thought of this for someone's dead little sister, maybe the game would have been a lot happier...
Attempting to do so during the battle with said dead little sister (at least the original PS1 version) gives you the bizarre message that you "missed."
This one is especially strange because even if she survived that battle, she would've died during the cutscene afterward anyway. Or in other words, there is no good reason even for the developers to not let you Phoenix Down her.
The reason you can't revive Tietra is because, during said fight, she suffers from an inherent status (nicknamed "Auto-Dead") that makes her immune to everything. "Everything" includes having an HP count above 0.
In Final Fantasy IX Queen Brahne dies in the arms of Garnet/Dagger. At this point not only your party shall have a Phoenix Down, but this character already has a couple of healing/reviving spells.
Both Chrono Trigger and Suikoden had deaths that could be reversed via time travel, if someone did the right things. In Suikoden II, if you fulfill the requirements the dead person turns out to have literally been hiding the entire time.
In the Chrono Trigger example, other special circumstances are required beyond just time travel to pull it off, explaining why other deaths can't be reversed. The specific mechanism for time travel in CT usually only allows you to travel backward or forward by very specific amounts of time. For example, you can travel back exactly 400 years from the "main" time period of 1000 AD, but you can't "redo" events you've already seen in the 600 AD period by traveling back 400 years and 1 day.
In Suikoden, on the other hand, the time travel event is explicitly a one-shot deal. It can never be done again, meaning that other major characters who die later are dead forever. And the event can also only be used to bring back one of the current "108 Stars of Destiny", meaning that there's no option to revive the hero's childhood friend Ted, his mentor's girlfriend Odessa or his father Teo instead of Gremio. One of those three used to be a Star of Destiny, but he's not one of the current set, so it doesn't count.
Neverwinter Nights 2 doesn't let you bring Shandra back. Though the implication from Elanee's dialogue (if she is in your party at that point) is that normal resurrection spells actually revive people who are almost but not quite dead, and Shandra was way past that point by the time you get to her. In a more meta sense the game actually has no resurrection magic without expansions except for an item you get much later.
Various non-player characters in The Elder Scrolls IV: Oblivion cannot die until their role in a given plotline is fulfilled, if then. For example, you can range up and down the Archmage's tower in the Imperial City, killing key members of the Guild, over, and over again. Or go to the Imperial Palace, and cut down Chancellor Ocato until your weapon breaks. Most of the rulers of the cities of Cyrodil are likewise "immortal", save for one. Note that in Morrowind it was possible to kill plot-relevant NPCs, and in so doing, break the plot.
In the first Expansion Pack for The Elder Scrolls III: Morrowind, before the designers came up with truly immortal NPCs, they simulated the effect by giving the king a magic ring that makes him like unto a god. This was probably necessary because the king in question was such a Magnificent Bastard that otherwise even the most saintly PC would have been tempted to indulge in a little regicide. The fun thing is that this ring also made killing the king even more tempting, as the player would be able to loot it for himself.
Unfortunately some of the unkillable allies in oblivion are seriously lacking in skill, 'dying' over and over again during various missions, this can ruin the immersion somewhat.
Heavily subverted in the eroge-SRPG, Genrin no Kishougun 2. When characters die in combat THEY ARE DEAD FOREVER, not only can you not use them again but they can't even appear in story related sequences, which is particularly frightening in the fact that all but one of the first heroines introduced are your main combatants. Don't let them die.
In one of the endings in Baldur's Gate II and its Expansion Pack, Viconia is eventually assassinated by the Drow society that she had fled from by means of poison. However, throughout the game there are numerous people who have resurrection spells to bring back the dead, and you can even get a ring that renders its wearer immune to all poisons. Viconia herself is such a spellcaster, and even if another character is an epic level cleric, she's Killed Off for Real. (It should be mentioned, though, that if a character you are engaging in a romantic subplot dies and is resurrected in the game, it breaks the romance...for some reason. It is also possible for a character to be killed beyond the means of magic to revive them, but this normally requires spells like disintegrate, or such massive damage that the character is chunked.)
The games also have some cutscenes (in particular the battle at the end of the prologue in the first game) where a character is killed in actual combat... except that he simply drops dead after a while, even if the enemy wasn't hitting him/her at that point.
In addition, at the beginning, you find Khalid, Jaheira's husband, dead. Jaheira claims that it's no possibility of getting him back, since your captor had dissected and desecrated his body. Which was partially true in D&D at the time: Only a Resurrection spell — a 7th level priest spell — would work on saving someone whose body is dissected (which would be a fine limiting factor if not for the unfortunate fact that every temple in the game sold them and at least two Rods of Resurrection are on sale in the local adventure mart). The fact that Khalid's body stayed in Chateau Irenicus when it colapsed seals the deal, though.
Averted in Planescape: Torment. When characters are killed during cutscenes, fights still take place true to game mechanics, with damage listings and all. When your companions are all killed at the Fortress of Regrets, you are conveniently not there to Raise Dead.
In SD Gundam G Generation DS, the Rival Route is accessed by imitating the novelization of Mobile Suit Gundam; in other words, someone other than Char has to deal the last blow to Amuro, which kills him rather than simply damaging the Gundam as per the anime.
In Persona 2 Innocent Sin a friend/lover of Yukino dies by bleeding wounds. Even though they didn't try to use magic here to heal him, they did try when Maya got stab by the Spear of Longinius at the end. She too didn't live due to the spear being able to cause wounds that can't be healed.
In Persona 3, Shinjiro, Takeharu Kirijo, Shuji Ikutsuki, Jin, and ultimately, the main character.
Although in Shinjiro's case, playing as the female protagonist in the PSP remake can avert this. If you max out Shinjiro's Social Link, you can give him a gift watch that will stop the fatal shot that should have killed him. This is largely why Shinjiro and the Female Protagonist have become a Fan-Preferred Couple. Unfortunately, he falls into a coma and does not wake up until the final day.
Lampshaded in the RPG Dungeon Siege: You are given a mission to find an elder. When you arrive there, a cutscene plays where he is killed. When you return to town to report the elder's death, they ask you why didn't you just use one of your potions of revival to bring the elder back to life.
The PC RPG Arcanum: Of Steamworks & Magick Obscura has a NPC companion dying (well, if you manage to find him after he decides to leave the group at one point) as a part of his personal storyline. He can be resurrected, although his skills and personality change slightly in the process (and technologist characters have to be prepared for their deaths and create their resurrection gadgets in advance).
In the Ultima series, the player's party members die and get resurrected all the time... with two notable exceptions. In Ultima V, a character slain by evil king Blackthorne's pendulum is permanently dead. And in Ultima VII Part II, a sacrifice is required for the Balance Serpent, for which one of your party members volunteers who will then be gone forever. Until the much-maligned Ultima IX. *sigh*
In an interesting example, Phantasy Star II uses cloning as the preferred "revival" method of fallen characters - why a plot-killed character can't be cloned is vaguely explained in the US version by stating she can't be cloned because she's not human, even though cloning prior to this point works on her; a line in the original JP version states that the data required to revive her has gone missing; after the destruction of Climatrol and the death of Neifirst, the technology used to create biomonstersis no longer available on Motavia. The Japan-only PS2 remake adds an optional side-quest to fix this.
Bit character Tiem is murdered by her father Darum at the North Bridge when Rolf & co. bring her to see him; it's all a bit strange, since Tiem refuses to remove the veil obscuring her identity, and she mouths off to him when he demands the "stranger's" money, prompting him to slice her in the stomach. After he sees what he had done, he commits suicide, thereby letting the party continue on towards the Biosystem Labs.
Also in Phantasy Star IV, Alys is struck by an attack that's used repeatedly in the battle proper, but when it hits her in the plot, the effects are lethal. This is certainly an example of Gameplay and Story Segregation, however the 'lethal' result is interesting in that Alis doesn't die immediately - she becomes sick, and dies slowly over the next few (in-story) days/weeks - an attack that in most RPGs would either kill you or not, actually killed because of side-effects such as infections that most games would just ignore. This attack also seems to suppress healing abilities; the party healer attempts to heal her in the cutscene that follows, only to fail..
In Sword of Mana, the main character has to kill Amanda after she is bitten by Medusa. They try to bring her back using healing magic, but it only gives her enough time to speak a few final words before dying. One is left to wonder why they didn't try an Angel Grail instead.
There are several of these in Mass Effect: Corporal Jenkins gets gunned down by Mecha-Mooks right at the beginning of the game's first battle. Nihlus gets shot in the back of the head by Saren. And on Virmire, Shepard must choose whether to save Kaidan or Ashley; the one not chosen dies in a nuclear explosion. Wrex can also be killed in a cutscene on Virmire, but it's probably more of a Final Death than a Plotline Death, since whether or not he died depends on the player's choices.
In the finale of the sequel, choosing poor teammates for specific tasks will get them (or another character) killed in a cutscene. Also, Mass Effect 2 has to enter the history of video games as a game where you can actually put your handcrafted AFGNCAAP character through a Plotline Death (disregarding the fact that he/she dies in the beginning of the game).
The third game guarantees the deaths of Thane and Legion; the former is guaranteed to go out like a badass, while the latter will either make a Heroic Sacrifice or be killed to stop him from killing you, depending on the choices you make. While a lot of former allies, and even some current ones, can die over the course of that game, these two are the only teammates who are guaranteed not to make it to the ending under any circumstances.
Valkyrie Profile: Damn near everybody. But in a sort of inversion, since you're playing as a Valkyrie, that's how everyone joins your party.
In Tales of Symphonia, the party healer's failure to save a dying NPC is Handwaved as healing magic being less effective on people without Exspheres. But it was always completely effective on Genis and Colette even before they got theirs.
Nevermind Zelos's death if you choose to end the game with Kratos. He has access to both an Exsphere and Cruxis Crystal. This is Handwaved by no characters even attempting to save him. Of course, in that ending he had just betrayed the party, so bringing him back to life might not have been the best strategic decision. And he turns out to be a Death Seeker, as well - hardly someone you want to be relying on in future battles, in either case.
Tales of the Abyss will always include Replica No. 7 Ion dying. Whether he was a Death Seeker at that point is debatable - he was ready to heal Tear, which would've put his own life at risk. Luckily, Anise's betrayal had given him a wonderful excuse for a Heroic Sacrifice to help the party get rid of the miasma and heal Tear, too.
In Tales of Legendia, the party healers try to save Stella after she has her spirit bird Teriques eat a cannon beam, but she's apparently too far gone for healing Eres to have any effect. So much for that Romantic False Lead. Later on, when Fenimore is stabbed, Maurits orders his men not to heal her in hopes that this will create impetus for Shirley's powers to awaken. She dies. It works.
Wizardry 8 has this in spades. When a PC gets killed, you can resurrect him/her with relatively little effort (Resurrection Powder). Should the same happen to an NPC, he/she is gone (with a rather gory explosion, usually). A particularly egregious example is the death of Jan-Ette, a recurring NPC from the previous Wizardry, who you find imprisoned and dying on Bayjin. She actually manages to talk to your party one last time, then she simply collapses in a heap and vanishes from sight.
In Square's Saga Frontier 2, most of your characters will die in plot deaths fighting in battle, due to old age, or due to illness. Granted, the game spans almost a century (Only one character is shown to have lived to experience the entire game).
Johan in this game is a good example of a Plotline Death that avoids Gameplay and Story Segregation. Characters in the game die if their LP runs out, and during Johan's final sequence, his LP slowly ticks away to zero due to a poison as he fights hordes of incoming monsters. Annoyingly enough, main character Gustave dies in the EXACT SAME place and time, from the EXACT SAME HORDE OF MONSTERS without ever getting a chance to fight properly.
In Valkyria Chronicles, despite the fact you have a medic that can revive teammates who have taken tank shells to the face, Isara dies of a single gunshot. The medic is nowhere to be seen.
Pokémon battles only ever lead to Pokémon fainting, and they can easily be revived at a Pokémon Center. Cubone's mother in Pokémon Red and Blue was just the first Pokémon character to explicitly die - various Pokémon graveyards exist, for one thing.
Completely averted in Fallout. When a character dies, they STAY dead.
"Dogmeat has died" Crap, quick load! Stupid dog!
Played straight with Essential NPC's in Fallout 3, who have Gameplay Ally Immortality and can only die in cutscenes or scripted events (e.g. James' sacrifice at Project Purity).
At the beginning of the Fallout: New Vegas DLC Honest Hearts, the Happy Trails caravan is attacked by tribals. No matter how fast you take out the bad guys, the caravaneers are scripted to drop dead.
Modus operandi of Dragon Age: Origins, it seems. All fights in the game are essentially the same, so whether a character is to die or simply be captured, the individual event happens in a cutscene after the fight, and sometimes when they have been lying dead in a pool of blood for half the battle.
In Shin Megami Tensei: Strange Journey the first sector has Gore killed in a cutscene. Interestingly just before this there is a cutscene fight which visually is a perfect mimic of game battles, but he is killed outside of battle. Unlike most examples, humans can't be brought back through the common resurrection item.
One of the bosses in Sion's campaign in Treasure of the Rudra has an ability called 'Foxy Killer' which it uses to force one of these. Foxy can't be revived by usual means after being hit with this skill, only by a trip to the underworld.
Ace Combat deaths (for anyone but yourself) only happen when the story says that they happen. Unlike Gameplay Ally Immortality, this applies to enemy NPCs as well. For example, in Ace Combat Zero: The Belkan War Erich Hillenberand will always survive you shooting him down (in fact his first line is about him ejecting as you opened fire), while Anton Kupchenko won't; same goes for Ilya Pasternak who is killed in Ace Combat 6: Fires of Liberation. A twist in Zero is that your story path determines whether or not Alberto Lopez survives being shot down, although this is inconsequential to the broader story. In any case he ends up dying anyway, with the story path only determining how long it takes to happen.
Also done in Ace Combat 5: The Unsung War with one of your squadmates and an enemy. If you shoot the named enemy in the second-to-last mission there's a comment about you being the ace of aces, but the enemy still appears during the final sequence to get his final Karmic Death.
In the original Wing Commander, if a character died, they were gone for good, sometimes resulting in you having to fly missions solo. (Given wingman AI, however, it could be argued that you were always flying solo.) Starting with second game, pilots who get shot down eject, until the storyline calls for them to die.
In Assassin's Creed II, you could've totally saved your father and brothers with a fair bit of skills and some attempts, but they have to die during a cutscene and your sword had totally be knocked out of your hand even though you could easily pick it up/dodge the attack if it's in gameplay.
In Silent Hill 2 there is no way to prevent Maria's death in Brookhaven's basement.
Or in the jail cell. Or in the room with the Pyramid Heads. Or when you fight her, on some endings, anyways.
The Fatal Frame games tend to conclude their (generally canon) endings with a Plotline Death. In the first, Mafuyu stays behind with Kirie, effectively killing himself to be with her; in the second, Mio strangles her sister Mayu to death as part of a ritual; and in the third, Kei (Mio's uncle) is captured and killed by the Tattooed Maiden, with Mio left in a perpetual coma ever since the game's events. Good endings allow you to negate a lot of these, but again, they haven't been canon thus far.
Resident Evil: Code: Veronica has a distinct NPC scenario. Steve, having mutated into a large green monster, can take any and all damage thrown at him by Claire without missing a beat. But he gets killed by a tentacle. A tentacle that had its end chopped off. Wut?
The original Resident Evil has poor Richard Aiken die, despite a Hope Spot being around in the form of finding a serum for him (he's poisoned). In the original game, you'll just get a radio if you give him the serum on time, while in the Gamecube remake, he'll live, but he'll either be killed by the snake Yawn (Jill's scenario) or a Neptune shark (Chris' scenario) shortly after. In the remake, having him die the latter way will net you his assault shotgun, however, so it's worth it to get him the serum.
In Ib, there is no way to save both Mary and Garry. One of them will die no matter what. Garry will either be driven incurably insane and left to die or he'll be murdered by Mary, and in a playthrough where he survives Mary will be set on fire. It's also possible to end the game with both of them dead, and in a really bad playthrough Ib will die too.
Fire Emblem Jugdral, Sigurd, main character and Lord for the first half of the game dies on you at the end of a chapter. Along with his entire army except for one or two survivors. Fortunately, all the ladies left children behind to carry on the struggle. Two children each, in fact.
And there's a justification as to why you couldn't use the Dead-raising "Valkyrie" Holy Stave— when you get the wielder of the Staff, Claud, he says that it cannot raise those who have lost their Quintessence, which happens slowly over time, or could be stolen by special weapons... by time you get another Valkyrie wielder, the first gen characters have been dead far too long.
In Sword of Flame, Ninian (playable character) and Hector's brother Uther (NPC). We also have Eliwood's father Elbert and Matthew's love Leila (both NPC) who also suffer deaths without any chance to save them. Ironically, in Binding Blade, we had Hector becoming the embodiment of Plotline Death.
Ninian got resurrected again though, and lived happily ever after, Athos was the true plotline death in that he apparently overdid it in the fight against the Dragon, regardless of whether or not you actually used him.
Also, Lord Helman (Lord Elbert's friend who gets stabbed by Ephidel, becoming the first victim of the Black Fang in the game)
In Radiant Dawn (for at least your first playthrough), Pelleas.
In Fire Emblem Akaneia, your decoy in the fourth part of the Prologue, and Marth's parents. The sequel subverts the Decoy's death, as Frey (The canon decoy) shows up alive and kickin'.
In La Pucelle, Alouette the Maiden of Light uses the last of her power to help Prier purify Croix's (the Dark Prince) heart and passes on.
In Jeanne D Arc, one would naturally expect the lead female to be burned at the stake. However, since Jeanne herself had already gone MIA, and the French higher-ups made her childhood friend Liane pose as her for the remainder of the war... Although Team Pet Cuisses inherits her stats via the Paragon's Armlet, Liane only comes back as a spirit to assist in a Battle in the Center of the Mind against a demonic duplicate, and the player can recruit her ghost as a post-game bonus. Nevertheless, she remains legitimately dead to the plot, and Jeanne and Roger are last seen praying for her at the Chapel near Domremy.
But they have also toyed with us with this trope. Axel Almer and Alfimi were supposed to be Killed Off for Real after Original Generation 2, yet they came Back from the Dead when OG Gaiden rolls in. Likewise, put one of your character a Defensive Support skill, and get him/her near Kyosuke during the last mission of the bonus section of OGs. Lamia Loveless would still get killed... until OG Gaiden rolls in and it's revealed that she's only Not Quite Dead. Considering all these examples span in the period of two games, it could count as before OG Gaiden gets released, people thought these characters are goners.
Another version of toying around: According to Compact 3, Fernando Albark, Maysis Mark and Alion Lucada are supposed to suffer Plotline Death, there's no way you can save them. But their stories get tweaked that they didn't die. Fernando and Alion ends up joining you for good, while Maysis takes the back seat. Likewise, this also happens to Despinis, who ends up doing a Heel-Face Turn before she could get killed, ensuring her survival.
And for non-OG examples (for this instance, Z), we have Setsuko's teammates Toby Watson and Denzel Hammer, killed by Asakim Dowin to further traumatize Setsuko.
Baldarov from Warsong (Volkov in the original Japanese version of Langrisser) is struck down by an assassin's arrow at the end of Scenario 5, forcing the hero Garett (Ledin) to continue to journey on his own. Hopefully, you'll have given him an opportunity to level/get promoted before Baldarov/Volkov's inevitable death.
In Luminous Arc 2, you may have battled and beaten him plenty of times, but Master Mattias only died in a cutscene, complete with a special CG.
Odium: Poor Joan McFadden. Killed almost instantly by a poison which inexplicably was particularly deadly and immune to antidotes on that occasion. Too bad that her corpse and everything she was carrying vanished mysteriously shortly thereafter, too. But not before she delivered some annoyingly narmy lines.
So when the king is killed in the very beginning of Shining Force, why exactly can the local priest not revive him? Even worse, since he didn't die right away, why can't you just HEAL HIM?
Future Tactics has one glaring example of Gameplay Story Segregation in this regard. At first if you lose a single party member it is an instant game-over. A ways into the game, however, you obtain a device that will resurrect any dead party member, and in subsequent fights you only lose a party member for the remainder of the battle if one dies. Then, in a cut scene Pepper is killed by a stray grenade, and remains very much dead even though the immortality device was a huge plot point.
In Saints Row 2, Carlos could have EASILY been saved. How? Shock Paddles, some food, walking it off, or calling 911 for an ambulance. Though he does come back as a zombie, and since Zombie Lin from Saints 1 is canon (some goths mention her, and the Boss says he tried to sell the story to Channel 6 in one of the DLCs) then so is he.
Johnny Gat suffers one early into Saints Row The Third, being gunned down by the Morningstar gang offscreen and returning a a zombie Homie at the end of the game, which in the series denotes a character that's Deader than Dead. Taking note of the word "offscreen," the dev team made a saving throw in the next sequel by revealing that Gat actually survived after all.
A version of this occurs in Little Big Adventure II. Normally, non-villain characters in the game can't be killed, and most of them won't die even if they accidentally get whacked by a villain aiming at the hero. However, at one point a dissident escaping prison with you gets shot before he can get out of the building, and dies. An interesting thing about this is that your character possesses some sort of a healing ability, and the dissident doesn't really die instantly after being shot — but since the event happens during the cutscene, there's no way you can save him.
Grand Theft Auto: San Andreas. A character who has the oomph to resist multiple bullets moments ago (on the roof of Madd Dogg's mansion) gets taken down by a single bullet in the foyer.
This can happen in tabletop games too, if your GM decides to unleash The Plot Reaper on an important NPC. Even if one of the PC's has healing abilities, they will not be able to help. Resurrection will be completely out of the question. Of course, this works better if the game is already very cinematic/story oriented.
The spell's description explicitly says that a person can only be brought back if they want to come back. Since the afterlife is usually a great reward for most people, they usually only come back if they have something important to finish. The GM usually doesn't have to pull any tricks - it's not difficult to argue "no, he's happy where he is and doesn't want to come back."
Using this excuse too often on beloved NPCs is likely to result in the players walking out in disgust though.
There are games besides Dungeons & Dragons, which all of the above comments reference. In most other games death is not reversible or pretty much guaranteed to hit Came Back Wrong. For instance, in Call of Cthulhu, if the GM decides a cultist with a hunting rifle picked off the important NPC while he on his morning jog, well, he's dead. Of course, used poorly, that's a sign of a bad GM. Used well, it can force the players to seek out new ways to get the job done while helping enforce fear. Tropes Are Not Bad, and Tropes Are Not Good, after all. A good GM generally lets player input change whether or not The Plot Reaper can harvest someone while the players are around and is ready for both contingencies. Sticking with Call of Cthulhu, a GM could easily set it up so if the important NPC lives, he can tell the players important info, but if he dies, it's found in his journal which he wills to one of the characters.