The Carpenter in Alice: Madness Returns, all of his actions involving sinking ships and building an underwater town were to protect his part of Wonderland from the Infernal Train. Said train smashes its way through the Carpenter's theatre, and he moves himself into its path so it doesn't hit Alice.
While most Templars earn sympathy for their earnest beliefs that they're making the world a better place, sympathy for the penultimate Templar target, Sibrand, is earned because of how pitiable he comes across at his death. Of all the Templars he took the knowledge of the Piece of Eden's existence the hardest. Believing the Apple was proof that God didn't exist and that there was no afterlife, Sibrand goes through a steady Villainous Breakdown brought on by paranoia that Altair would kill him just like he did to the rest of the Templars. By the time of his death, Sibrand is so crazy that he's firing at white birds because he's afraid they might be Assassins, and his final words display just how horrified he really is at the thought that he will no longer exist.
This actually happens so often in the first game, that one of the most notable assassination targets is an aversion of this trope. When Altair asks Majd Addin if, like the other Templars, he'll try to justify his crimes as being done for a greater good, Addin merely scoffs at him, saying that he murdered people for fun, because it made him feel like a god. Altair, who has been steadily becoming sympathetic towards his targets as the game's gone on, decides to show Addin exactly what happens to people who put themselves above others by shanking him in the neck.
While most of the Templars in Ezio's tale have turned from Well Intentioned Extremistsinto power-hungry murderers and schemers, at least some of his enemies still manage to be sympathetic, such as Dante Moro. Friend and bodyguard of Marco Barbarigo, Marco eventually decided that he wanted Dante's wife for himself, and put a hit on his "friend" in order to get her. While Dante survived, a stab wound delivered to the head resulted in him being brain damaged, which Marco exploited in order to get Dante to divorce his wife. As an easily malleable tool for the Templars, Dante falls to Ezio, but seems to gain some semblance of his old self in his last moments, helping Ezio by telling him where the remaining Templars have fled. His death delivers an additional punch when Ezio finds a letter written to Dante from his ex-wife where she expresses that she still loves him, has never given up on him and now, with Marco dead, she promises to help him get his mind back.
Girolamo Savonarola, a monk not affiliated with either the Templars or the Assassins, he gained possession of the Apple of Eden and used its power to take control of Florence. Being a Well-Intentioned Extremist trying to purge Florence of everything he viewed as evil, it's hard not to feel bad for him when he's defeated and nearly burned alive by an angry mob. Even Ezio pities him enough to deliver a Mercy Kill rather than let him die in such agony.
Haytham Kenway, the father of protagonist Connor, dies following a duel with his son. Having spent so much time futilely trying to convert Connor to the Templar side, he acknowledges, in his own way, that he's proud of his son for the admirable qualities he's displayed. Connor takes no satisfaction in his death, and it's quite a sad sight to see when Connor arrives at his funeral where Haytham's mourners are weeping and Charles Lee is delivering an impassioned eulogy on what a good man he was.
It gets worse in context: Assassin's Creed: Forsaken reveals that Haytham had actually been trying to pull a You Shall Not Pass! to save Lee from Connor, and if the player has Connor return to the basement cellar of the Davenport Manor afterward, under Haytham's portrait is written "Sakataterihwáhten◊" — a seemingly common translation of which is "I made a mistake."
Charles Lee, despite being Connor's Arch-Enemy and a cruel Smug Snake, also gets a sympathetic death. Unlike nearly every other assassination target, Lee has no final words. Instead, after his friends are dead, his plans are foiled, and he's been gravely wounded by Connor, Lee flees and eventually takes refuge at the Conestoga Inn. However, Connor manages to track him down. Faced with his imminent death, Lee reacts with dignity, wordlessly sharing a drink with his nemesis before giving a nod to Connor to let him know he's ready.
Benjamin Hornigold defected to the Templars because he wanted to make the world a better place after seeing Nassau devolve from the democratic society he and his friends first envisioned it would be into a Wretched Hive. Though treated with contempt by Edward for his betrayal, Hornigold still attempts to warn Edward about how lonely and empty his life will be if he keeps going down his selfish course. By the game's end Edward has made peace with his deceased friend, as he imagines Hornigold sitting at a table drinking with the rest of their friends they lost along the way.
Bartholomew Roberts, the merciless, Wild Card pirate not aligned with the Templars or the Assassins, faces his death with dignity, always knowing that his life would be a short one but a merry one. The only regret he has is that he was Born in the Wrong Century and that, because of this, this incarnation of him would never be reunited with his one true love, Juno. Just before dying he asks Edward to dispose of his body, knowing that the Templars would use it to control the Observatory for themselves.
Assassin's Creed: Syndicate: Jacob assassinated the railway mogul Malcolm Millner... only to realize that he was fighting the Templars. Jacob's been helping a Templar regain her fortune all along. Whoops.
Baldur's Gate's Irenicus is rather pitiable in his final moments. Even more so is Yoshimo.
Baten Kaitos Origins does this for almost every villain in the game, with the exception of the game's biggest monster and the one who was horror incarnate. This is particularly notable in the case of the Big Bad and his Dragon, both of whom had their daughters crying over their bodies as they died, but it also shows up in the deaths of the rest of the major villains - such as Nasca, who fought despite knowing it was practically suicide simply because "Heughes would never let me live it down!" Then you get to Heughes... who does the same thing because running away would be a bad example to set for Nasca. Though technically, it's the player's choice whether or not to fight and kill Nasca, Heughes, and Valara. And if you choose not to, they each pull off different but equally awesome Big Damn Heroes moments at the end of the game.
At the end of Batman: Arkham City, he's been around two games while kicking dogs and generally doing his best to piss you off. However, the death scene of The Joker is surprisingly sad, even when you know he had it coming.
Batman: Do you want to know something funny? Even after everything you've done... I would have saved you. Joker: (By now laughing and coughing uncontrollably) That actually is... pretty funny...
Poison Ivy's death in Batman: Arkham Knight is also very poignant. Despite ranting about how much Humans Are Bastards, her final act is a Heroic Sacrifice, clearing the city of Scarecrow's fear toxin, saving countless lives, and simultaneously rescuing the trees she cared so deeply about. In the end she became a hero.
Ivy: (As she dies in Batman's arms) Nature always wins.
Quincy Sharp may have been a Sleazy Politician and an Ax-CrazyKnight Templar who approved of some evil deeds in past Arkham games, but when you find out that he was Driven to Suicide for realizing his misdeeds at the urging of a hallucination of Hugo Strange while facing punishment for his crimes in prison, you'd probably feel a little depressed at how his life fell apart so fast. This is only made worse by the fact that his motivation was to become Gotham's hero like Batman.
The Big Daddies. After you kill one, its Little Sister runs up to the corpse, crying and asking for it to get back up again.
The Alpha series, those bastards who attacked with no warning. You're going to feel like a true Heel when you learn the reason why they're so suicidal. They lost their Little Sister, who was their whole world. Later, you're treated to the fact that one of them spent the remainder of his life crying next to a Gatherer's Garden. Almost makes you want to kill them just to put them out of their misery.
And then there is Andrew Ryan. He's definitely set up as the main antagonist during the first part of the game (he tries to kill you multiple times), but his death is too jaw dropping for words. He gives Jack commands punctuated with "would you kindly," the phrase Jack's buddy Atlas has been using over and over; it's seemed like an endearing little turn of phrase up until the moment when Jack powerlessly obeys all the commands Ryan gives him — it's Jack's Trigger Phrase, and he's unknowingly been a Sleeper Agent who is now being pulled this way and that by Atlas, who is actually Fontaine. Ryan is obviously disgusted by this as it contradicts everything his Objectivist philosophy stands for, summed up neatly in his faborite saying: "A man chooses, a slave obeys." At this point he "asks" you to kill him, knowing that Jack is his own son, taken from him from birth by his worst enemy and turned into an assassin. Though Ryan's motives are famously ambiguous at times (something others comment upon in game), he sacrifices himself in order to show his son that he's being controlled, shouting "A man chooses, a slave obeys!" as Jack helplessly beats him to death.
Songbird in Bioshock Infinite who Elizabeth is forced to kill near the end to protect Booker, by transporting the three of them to Rapture. He's stuck outside the glass, and Elizabeth comforts the one guardian and companion she had for her whole life trapped in her tower as he slowly succumbs to the enormous water pressure and slowly sinks to the bottom of the sea.
In Black Mesa, in comparison to the original Half-Life, the U.S. Marines hunting the Gordon Freeman are portrayed much more sympathetically and tragically. In particular, the remade sections of the chapter "Surface Tension" show their doomed two front fight against Freeman and the Xen invaders in a more sad and horrific light, with new radio conversations illuminating the Marines' desperation as they're being overrun. The final one is of a dying Marine and the corpsman who's trying to save him, only for the dying Marine to stop responding.
Interestingly, Cave Story doesn't do this for the Big Bad, but for the little guys. In the standard ending, the cutscene features a slow pan over the various levels of the game and all the enemies in them, set to sad music. Then, the floating island they're on crashes. Also, Misery, except in the perfect ending.
Magus, should the player decide to fight him at the North Cape. With his dying breath, he tells the party how to revive Crono and drops the amulet his sister had given him as a child. She had promised it would protect him from harm...
Then we have Azala, who had been waging a war of extinction against the prehistoric humans, and eagerly anticipating Lavos' imminent planetfall. However, her last words are not to curse her opponents, but to lament that her people never had a future and accepts her species' defeat without a Villainous Breakdown. Though she's a villain she was simply fighting for the future of she and her people, not that different than the humans, which actually moves Ayla of all people to show mercy and offer to rescue Azala: an offer that gets rebuked because it's meant to be.
Criminal Case: Grimsborough: Of all people, The Rorschach Reaper somewhat gets this treatment. It's a complicated example, too, as she can also be seen as Asshole Victim given that she's a Serial Killer. But after the team discovered why she's killed, that she attempted to seek the truth about her ancestor's death and indirectly exposed the Crimson Order who responsible for said ancestor's death, she becomes less of an asshole. Even her sister who initially openly hated her for being a killer later admits that she does feel sad over her death.
The Great Wolf Sif in Dark Souls. He can't really even be called a villain — Sif is just having a knee-jerk reaction to someone trespassing near his friend's grave. Near the end of the battle, Sif even starts limping in pain as he valiantly struggles to protect Artorias' grave from an Undead monster (i.e., you). Sadly there's no way to spare him since you need Artorias' ring to proceed with your quest, and the only way to get the ring is by killing Sif.
And it gets even worse if you become his friend by saving his life with time travel; he has a duty to protect Artorias' grave, so you still have to kill him, despite the fact that neither of you wants to.
The Traitor's fall and death in Dawn of War II: Chaos Rising is treated sympathetically, but the deaths of Jonah Orion, Avitus, and Tarkus stand out in particular:
Jonah Orion is possessed by a Daemon and forced to betray your side, leaving behind a message in which he desperately pleads with you that he can't control his actions and to forgive him. When he finally goes down Fighting from the Inside against the Daemon possessing him, his former squadmates express sympathy for his fate, with Tarkus commenting that "The man who has nothing can still have faith."
Thomas and George from Deadly Premonition. Thomas secretly had a crush on George, and was jealous of Emily over the fact that George obviously cared for her. This jealousy was used by Forrest Kaysen to drive him murderously insane, forcing Emily to kill him. As for George...you wouldn't think he'd get a touching sendoff, given his actions, but then you realize that he only did the murders because the horrificCold-Blooded Torture his own mother subjected him to during his childhood deeply traumatized him to the point that he wanted to become strong above all else. Oh, and like Thomas, he was essentially being used by Kaysen. George's pitifulness is driven home during his Villainous Breakdown, where he tearfully calls out to his long dead mother, saying that it wasn't his fault and begging her to not to hurt him again...
Cliff Hudson from Dead Rising is a Vietnam war veteran who is experiencing war flashbacks due to the death of his granddaughter at the hands of zombies, and has become psychopathic as a result. When in his death throes, he snaps out of his madness, resulting in an extremely sad death scene. He is one of the few Psychopaths that most players regret killing, and notably the only one Frank himself feels bad about putting down.
The Starter Villain Daniel is an android who feels betrayed by his owners for replacing him, and to this end Daniel decides to kidnap the daughter of the family named Emma and becomes a Serial Killer. Although how sad his death is widely depends on how the player chooses to interact with him, if the player decides to give multiple promises to Daniel that everything will be fine, only for a sniper to shoot him, his death is taken very sympathetically and extremely tragic.
Of all people, Todd is given this in all of his defeats. If he is killed early on in the game, his insanity is played for sympathy and he comes across as more of a broken man than the evil man he is previously seen as, stating that he actually loves his daughter who he abuses on a daily basis. If he survives, he will return in the chapter "Battle for Detroit" and desperately scream "YOU STOLE MY LITTLE GIRL" when he finds Kara and Alice which already applies sympathy, but is given even more sympathy if Kara tells him about his backstory; His wife left him and took his real daughter away, leading Todd to buy the android Alice in order to cope with reality, but it all went wrong and he started abusing the poor android. Todd will start crying and hugging Alice, before telling a security guard who he earlier told that Kara was an android who was to be executed that he was mistaken and, although he doesn't die here and seems to redeem himself, he still lost Alice who he will never see again.
If he becomes a Villain Protagonist, Connor himself will have multiple possible deaths, and all of them are sympathetic. There are two standouts however. Captain Allen might return as Connor is trying to assassinate the Jericho leader Markus in the chapter "Battle for Detroit" and try stopping him from doing it, but Connor will instead try killing Allen and his mooks. Allen will shoot Connor multiple times and how utterly pathetic his death is and yet how loveable and Endearingly Dorky he used to be makes it hard to see him dying like that. There's also an example if Hank confronts him while trying to assassinate Markus and the two will start a fight, and although it possible that Hank is the one who dies, which is equally sad and a Moral Event Horizon for Connor, it might just be even more depressing seeing Hank throw him off the bridge after all of their Character Development together.
One In-Universe example is Leo Manfred. Although he is an Asshole Victim and Hate Sink for most of the players, if Markus decides to fight back when Leo picks a fight with him, Leo will get pushed into a lamp and faint, although he does actually survive if this happens as revealed later, he certainly seems dead, and Carl Manfred, his dad, comes up to him to hug him and say "my little boy... Leo...", which is tragic, as stated, In-Universe and most people saw his presumed death as nothing but deserved.
Deus Ex: De Beers by all accounts is a terrible, classist man whose actions during the 20th century and during the beginning of the 21st lead the world into the state that it is in. That being said, it's hard for some to not feel sorry for him when the player learns that Morgan has no intentions of curing his diseases and plans to leave him in a cryopod indefinietly.
After you defeat the recurring Worthy Opponent Nelo Angelo in the first Devil May Cry game, it's revealed that he was really Dante's twin brother Vergil. Vergil also qualifies for this in the third game, when he chooses to stay in the demon world after losing to Dante.
In Dragon Age: Origins, the moment when (if) Teyrn Loghain is executed is one of these, as his daughter weeps and begs for his life and he looks back saying that little girls never grow up and always have pigtails in their hair. Then she gets spattered with her own father's blood.
Dragon Age II has two major examples: Meredith and Anders (if you choose to kill him). Both started out as reasonable people who were corrupted by a combination of supernatural forces and their own prejudice or anger and both have tearjerking death scenes: Anders tells your Player Character "I'm glad it was you" before s/he kills him, with a look of anguish and remorse both before and after being stabbed. Meredith turns herself to stone in the midst of her Villainous Breakdown, permanently frozen in a nightmarish expression of rage and fear.
Many of the possessed Mages faced in the game. After being backed into a corner by the Templars, they resort to Blood Magic out of sheer desperation and end up becoming monsters. Made even worse where in some cases, Hawke arrives only a few moments too late to be able to save them, such as with Ser Thrask's daughter.
The Arishok. He spent three years stuck in Kirkwall and was unable to leave until he found the Tome of Koslun, thus fulfilling his duty to the Qun. It's heavily implied that part of his motivation for invading was to either cleanse the city of it's corruption or die in the process, with his Duel to the Death with Hawke being an intentional Suicide by Cop.
Dragon Quest V: In the DS version, it's hard not to feel bad for King Korol when Nimzo has Ladja execute him in an excessively brutal fashion.
In the Dynasty Warriors series, Cao Cao was always portrayed as somewhat villainous and cruel. However, in the seventh game, it showed that beneath the coldness, he does care about the people who serve him, and he does wish for the chaos to end. Right before his death, he pleads for Xiahou Yuan and Dian Wei (both of whom died serving their lord) for their forgiveness.
Ulfric: I'll never surrender Skyrim into the hands of a corrupt and dying empire! Rikke: Skyrim doesn't belong to you, Ulfric. Ulfric:No...but I belong to her.
Conversely happens with General Tullius as well, should you side with Ulfric. While a grumpy old jerk who clearly holds the Nords in disdain, Tullius fought to preserve the Empire because he truly thought it was best for Skyrim's prosperity and protection, and the only thing stopping mankind from being destroyed by the Thalmor. Once you've cornered him in Solitude, he's basically given up, though he'll still fight you. His Last Words are bluntly and resentfully telling Ulfric that he's just given the Thalmor exactly what they want.
In Fallout, this can happen with the Master if the Vault Dweller choses to convince him of the futility of his plan. He converted people into Super Mutants because he truly believed that they were the race best engineered to survive the wastes, and that by unifying everyone into one race, he'd be preventing humanity from tearing itself apart because of their differences. If the Vault Dweller can prove to him that his mutants are all sterile, and his plan can't work, he'll be hit with the full weight of his crimes, and commit suicide out of guilt and despair. His final words are particularly poignant.
The Master: "Leave now. Leave while you still have hope."
Comes up more than once in Fallout 4. It first comes up with Kellogg, the man who shot your partner and kidnapped your son Shaun when you trawl through his memories after you kill him and find that he lived a horribly cruel life and lost his own wife and child, which drove him to become a ruthless mercenary. Notable in that the Sole Survivor can either express sympathy for him or rationalise that he doesn't deserve it because he knew himself what it was like to lose the love of your life and your only child and chose to inflict that misery on someone else. It also comes up with Shaun himself, who is now an old man and head of the Institute, provided you didn't kill him before the final quest and didn't side with the Institute: he lies dying knowing that his own mother/father is about to destroy his life's work, still convinced that the Institute is the last hope for humanity. His last interaction with his parent is to bitterly tell them to leave.
In Far Cry Primal, Takkar and his tribe, the Wenja, must contend with Ull, the warchief of the Udam tribe, who constantly launch attacks on the Wenja "softbloods" to murder and consume them. Later on in the game, however, we learn that Ull has two children to take care and is desperately trying to save his tribe from "skull fire", a mysterious and lethal disease. The Udam are consuming Wenja because they think it will cure them of their disease. And once Takkar confronts Ull for the last time at his cave, once he gives him a lethal wound, Ull desperately staggers away from Takkar in an attempt to prevent Takkar from murdering his baby. Takkar, feeling Sympathy for the Devil, agrees to raise Ull's children for him to make sure they don't die of "skull fire" like their people, and respectfully says "Walk free" when Ull dies.
Surprisingly enough, Geese Howard from Fatal Fury. At the end of Real Bout, he receives a Power Geyser from Terry, which sends him flying towards the window. As he is about to plunge to his death (again), Terry holds his arm to save him. Geese simply smiles and shrugs him off, falling to his death while laughing.
In Garou, we learn he left his son Rock for Terry to take care. Probably because Terry could be a much better father that he could ever dream to be.
Kefka: Why create when it will only be destroyed? Why cling to life, knowing that you have to die? None of it will have meant anything once you do. Terra: We live to protect what we hold dear. As long as you have that, you can find the meaning on your own. Kefka: Meaning, schmeaning. The whole world's going bye-bye! You included! Life... Dreams... Hope... Where do they come from, and where do they go? None of that junk is enough to fulfill your hearts! Destruction... Destruction is what makes life worth living! Destroy! Destroy! Destroy! LET'S DESTROY EVERYTHING! [explosion, followed by a sobbing laugh] Terra: It was your broken heart. You were trying to fill it with destruction...
While Sephiroth doesn't recieve any outright sympathy, quite a few characters hint that his cold exterior is a result of a deep despair.
The end of Final Fantasy IX had Kuja dying at the base of the Iifa Tree. Being a fluke with a crushingly short life-span made him cruel and nihilistic, but only when he was defeated by the heroes and had nothing left to live for did he realize too late what it means to really live. This also gets a callback in Dissidia.
In the same game, Brahne's death is a surprisingly solemn moment. In spite of all the atrocities she did, Garnet still loses her mother when she dies. Although it's a little played with. While Garnet is (understandably) saddened by her death, the other party members (like Vivi) on the other hand feel sad for Garnet, not really for Brahne.
Final Fantasy XII: despite their eventual descent into madness, Cid and Vayne have some redeeming qualities, and Venat garners some sympathy:
Vayne is one of the most affable and - dare one say it - likeable antagonists in the series due to the inherent humanity behind his actions, and though he doesKick the Dog on occasion, he's a Well-Intentioned Extremistpar excellence with good emphasis on the "Well-Intentioned" part of that description. His genuine love and compassion for his cute little brother Larsa helps immensely.
In the case of Cid, it hits especially hard when the player realizes that Cid only started neglecting his family because Venat contacted him. Balthier is especially saddened by his death, asking him if there was no other way.
Venat exemplifies all the best aspects of the Satan Is Good trope - the compassionate Defector from Decadence to contrast with the Jerkass Gods, the genuine liking for mortals and a desire for them to attain self-independence (much like Prometheus), and the capacity for kindness when s/he sacrifices his/her immortality simply so that Vayne doesn't have to die alone; as such, they depart the world together and in some semblance of peace.
While only an optional boss, Fury will start crying upon his defeat.
Final Fantasy Tactics: Wiegraf Folles and his sister Milleuda, who both started off well-intentioned and were arguably more heroic than the heroes during Chapter One. Wiegraf eventually went too far, what with joining the Corrupt Church and selling his soul to the Lucavi, but still...Milleuda, in contrast, was sympathetic until the end - being forced to kill her to progress in the game is a notoriousPlayer Punch.
Isilud Tengille, who wasn't even evil - when he realised he was on the wrong side, he tried to stop his father-turned-demon, only to be unceremoniously killed, followed by asking Ramza's sister Alma to send Ramza his apologies for having opposed him.
Both Confessor Zalmour Lucianada and High Confessor Marcel Funerbis had incomplete information, and seemed to genuinely believe they were doing the right thing. Zalmour goes out with a commendable dignity as he prays to God - not the Lucavi demons - to punish the wicked for their sins, and Funerbis swallows his pride as he begs Ramza "the Heretic" to stop the demons (after having been run through by the Big Bad and his minions despite pleading for his life).
The final rank mission of San d'Oria in Final Fantasy XI ends with this trope. With Prince Trion aiding your party in the fight, the head of the Orcish tribes, Warlord Rojgnoj, falls at your feet. In the FFXI universe, the orcs are beastmen who patrol various regions of the game, attacking adventurers at will - their reasoning for this? The very sword that Trion wields, one with enough power to separate a peninsula from the mainland and driving the inhabitants of a former powerful city underground. Rojgnoj tells all of this to us in broken English (or Japanese or French, depending on where you're playing from) and tells us this was the cause for the orcs waging war against the Kingdom of San d'Oria 20 years ago. It caused him and his people pain, and they simply wanted to destroy it. He dies shortly afterward.
Final Fantasy XIV has several sympathetic villains and has given them touching send-offs:
Zenos yae Galvus is a vicious Blood Knight who terrorizes his subjects in the hopes that someone will rise to give him a decent fight, yet his death is a sombre moment. When you defeat him, he admits that this is the first time he's ever felt joy in his life, and bids youhis first "friend"a fond farewell before slitting his own throat. Its then subverted when he comes Back from the Dead.
Emet-Selch, the Arc Villain of Shadowbringers, is a Well-Intentioned Extremist who is trying to bring back everyone who died when the original world was split into the Source and its thirteen Shards. When you defeat him and land the killing blow, his Last Request is for you to remember that his people once lived: once you agree to do so, he fades away with a smile as melancholic music plays.
Emet-Selchs colleague Elidibus likewise gets a touching sendoff in Patch 5.3. After you defeat him, he reverts to his true form as a small, childlike figure, and he finally remembers what hes been fighting for all these long eons:
"Yes I would become Him. I would save everyone. This I believed. Yet still they cried out, in rage and despair Dividedover the fate of the star. A rare occurrence, always fleeting. But not this time. Not this time Reconciliation. Elidibus. I was needed. I withdrew myself from Zodiark. For them My people. My brothers. (sheds a Single Tear) My friends. Stay strong. Keep the faith. At dutys end, we will meet again. We will. (struggling not to cry) We will. The rains have ceased, and we have been graced by another beautiful day. But you are not here to see it." (Disappears into Light)
The Fire Emblem series in general is quite fond of this trope. More specifically:
Fernand, who has been a Jerkass to the group the entire game, sees the error of his ways after being mortally wounded as a conequence of Berkut's Villainous Breakdown. His former friend Clive holds him in his arms and Fernand does what he can to tell him about Duma's madness and Berkut's own changes, and ask Alms to put Duma to rest. Then, Fernand aknowledges that his lack of forgiveness was his undoing, and dies telling Clive that he was right all along and chose the right king, Alm. Both Clive and his sister Clair are greatly distressed, with Clair telling him "Please Wake Up" and then sobbing. It's even worse if the player has a certain DLC stage that shows how Fernand USED to be before his Dark and Troubled Past hit him...
After both Berkut and his girlfriend Rinea (who had been turned into a Witch after Berkut sold her soul to Duma) are defeated, the mortally injured Berkut still refuses to give up or to see Alm as his cousin rather than his enemy, and urges Alm to give him the killing blow. But as Alm insists that he never wanted to be Berkut's enemy... Rinea's now-free soul appears in front of the group, speaking kindly to Berkut even after what he did to her, telling him to come with her so they can find their own empire. Berkut is flabbergasted and seems to be crying as he tells Rineathat she always was right, begs her to forgive him, and accepts her offer to go away with her. Then he makes peace with Alm and, before definitely dying, gives him a ring that belonged to his late mother and begs him to make Valentia a land where no one will be corrupted by the gods again.
Even a mini-boss in the final stage gets one. Hestia, one of Duma's witches, holds resentment towards her sister Sonya who ran away and averted being transformed, but regains her will as she dies and says she should've lived her life as she saw fit, like Sonya did.
The remake of the game adds Clarisse. Throughout the game, she's depicted as a sadistic, cold-hearted killer, who constantly abuses her adoptive sister Katarina for being useless. So one look forwards to the moment when she's finally fought... and her death comes as one of the most heart-wrenching moments in the series, specially when Clarisse quietly asks Katarina "Stay with Me Until I Die."
Eremiya. She's the one to blame for Clarisse being the way she is (and Katarina, and Roro, and Roro's clones...), then when it's time to finally beat the bitch, it's like a moment to celebra - what'sthis?! She once was a genuinely good person but Gharnef put her under Mind Rape when she fell into despair after witnessing the deaths of the orphans she originally cared for during the war, turning her into a Mega-Abusive-Bitch? And now, while she's dying, he completely restores her memories of who she once was, laughs, and lets her bleed to death in complete despair? ... Ouch. Just... ouch! For a character who didn't even exist in the original game, that's some pretty powerful woobie material right there. There's a very goodreason Gharnef earns more loathing than the game's actual Big Bad, Medeus.
In Fire Emblem: Genealogy of the Holy War, several people Tear Jerked over Arvis, who was actually similar to Lyon, and wasn't entirely the evil bastard he would appear to be if you took him in context. (One Freudian Excuse later) He was actually shown to be trying to stop the Child Hunts that were going on. Even Seliph, whose father was murdered by Arvis, later says that Arvis does not deserve to be demonized in history.
Galle, who was never your enemy, and was possibly romantically linked to one of your party members (though it isn't necessary to kill him) and Brunnya in the bonus chapters - fighting for a king already dead and knowing she only fights to be killed to stall your army. The final boss was a frail looking girl, though she gets better.
Despite being a veritable madman, King Zephiel - his final words, which verify his adamant belief that Humans Are Bastards is quite sad, particularly in light of the kind boy he used to be before his father's repeated assassination attempts screwed him up. Not to mention Murdock, who goes out loyally serving him despite being an honourable man who disagrees with the war as a whole.
All the major Black Fang members. Brendan, Uhai, Ursula, Darin, and yes, even Nergal himself, whose death becomes more pitiable depending on how many bonus chapters you unlock. The only Fang members you can completely hate at the end of the day are Psycho for Hire Jerme, Church Militant Kenneth, Evil Matriarch Sonia, and Ephidel, who probably has the most satisfying demise in the game.
And Kenneth and Jerme might earn a modicum of pity as well when you consider their appearance as Morphs in the finale chapter. It is implied by Eliwood and Co. that both men were driven insane by Nergal, especially when you consider that Jerme used to be the Fang's finest assassin before Jaffar joined the Four Fangs - Brendan had already shown he didn't tolerate sociopaths by locking up PascalGretzner (who deserves to be on the list of "completely hateable Fang members") in the past, after the man massacred innocents while gunning for his targets, just because he enjoyed killing so much.
Limstella: I am not human. This body and this heart are constructs. Yes, as is this sorrow.
Nergal himself also turns out to be this. At first, all he wanted to do was to find his missing wife, then reunite with his lost children. But Aenir was nowhere to be found, and with the Dragon's Gate closed, he began to dive deeper into the darkness so he can find a way to reopen it and see his children again... but slowly, the darkness engulfed him and eroded his mind completely, leaving him with no memory of who he was, or why he was even doing any of this; it all goes downhill from there for everyone, including Ninian and Nils, the very reason he chose this path to begin with. By the time you kill him in the endgame, Nergal has become so corrupted by his dark magic, he can barely remember his own name.
Selena - the good general hopelessly in love with her long-deceased Emperor.
Orson also qualifies. Despite betraying his homeland of Renais to the Grado forces, it's made clear that he only did it because the death of his wife broke him completely, leaving him open to manipulation by having her (half-assed) resurrection offered in exchange for his compliance. He becomes more physically-emaciated each time he appears, and in his last appearance (where you kill him), he's gone completely off the deep end talking to a shade of his wife - his last word is her name. Ephraim, Eirika and Seth all show sadness at how far he fell, not able to bring themselves to hate him despite all that he did.
The Black Knight. Yes, he killed Greil, but you still can't help but feel sorry for the guy.
Then there's his boss, Sephiran, a Woobie, Destroyer of Worlds and Death Seeker who's out to end it all because he can't see the good in the world anymore. The latter's cohort, Dheginsea is another example, as is Jarod, who for a relentlessly unpleasant Jerkass gets a surprisingly sympathetic send off, going down fighting after giving a Rousing Speech to his troops. The previous game has anti-villains Shiharam and General Bryce, whose death's cross the line into Player Punch territory, and Petrine who while an incredibly vicious bitch for most of the game, goes out so terrified that it's hard not to at least pity her.
Hetzel as well. Of all the Begnion Senators, he's clearly the least evil. (e.g., buying Rafiel as a slave only to save him and then release him.) Even when you do fight him, he apologizes and says he doesn't want to do it, he's more afraid of what Lekain will do to him if he doesn't go along with it. Data that has been found suggests that he could have been spared, actually.
Mustafa, a Plegian General who is so touched by the previous chapter's sacrifice that he does not wish to fight you, but must because his king, Gangrel, will bring harm to his family otherwise. Even before the battle starts, he realizes his own men don't feel like fighting either, and volunteers to take the blame for them if they choose to leave. It's actually this bravery in the face of punishment that makes them decide to stay until the end. It becomes even more of a Player Punch when you realize he was also the kind of general that was A Father to His Men. Not only are his dying words a plea to spare his men, but a conversation between Ricken and Plegian recruit Henry reveals that Mustafa used to give Henry a bag of peaches whenever he visited, because he reminded him of his son and even considered Henry a part of his family.
Mustafa: Well done, Ylisseans... Hrrggh! Please...spare my men...
Victor and Vincent are a pair of cheerful bandit twins who raid villages and have a very close relationship. If Victor is killed, the surviving Twin, Vincent is despondent and seeks to get his brother a grave after his Avenging the Villain is completed. While the whole thing was Played for Laughs, many players found it genuinely touching and sympathized with the bandit twins.
The Front Mission series is known for having these type of sad deaths with most of its supporting cast. Front Mission 3 is one of the better examples since you get to play two story lines which help show you the lives of those you end up killing or saving from new perspectives, including recruitable characters.
Ghost of Tsushima has Ryuzo. Yes, he betrayed Jin by siding with the Khan and the Mongols, and his actions had ultimately led to the death of Taka, but it's clear how much he regrets his choices in his final duel against Jin. At this point, his fellow Straw Hat ronin are dead and everything is crumbling around him, and all that's left for him is to go down fighting, instead of being beheaded as a traitor.
God of War III: Zeus. It's revealed right after his utterly brutal death by Kratos' hands that he was actually evil because he'd been consumed by the evils of Pandora's Box.
God Of War 2018: Baldur, a.k.a. the Stranger. His death by Kratos' hands to prevent him killing (an unresisting) Freya in revenge is treated as an extremely solemn affair. Besides how it devastates Freya, it leaves quite the impression on Kratos and Atreus, with the latter being dismayed to think that being a god will always end with children killing their parents like Kratos did and like what Baldur would have done, whilst Mimir solemnly comments there was no easy choice regarding Kratos' action.
The two major antagonists of Golden Sun: The Lost Age, Karst and Agatio, die of hypothermia in Mars Lighthouse after being turned into dragons and forced to fight the heroes until they're too exhausted and injured to warm themselves or escape. Agatio, The Generic Guy to the end, just tells the heroes to continue their mission and fire the Lighthouse for them. Karst, on the other hand, received just enough Character Development to shed sympathy on her Roaring Rampage of Revenge, so when she begs Felix to comfort her, it's both surprisingly moe for her and a flat-out Tear Jerker for us. Needless to say, a lot of fans rescue her in Fan Fiction.
Big Smoke from Grand Theft Auto: San Andreas gets some sympathy from CJ who is forced to kill him due to the former turning against the Grove Street gang. The two are implied to have been friends since childhood and Big Smoke going down the path of money, greed, and power only makes CJ solemnly wonder what exactly went wrong with his former friend and how it ended this way. Once said friend passes on, CJ can only utter "Damn...what a waste."
Trevor's death. On the other hand, one might not feel so bad about killing Trevor when you remember some of his actions... But being burned alive, screaming his head off, is a horrible way to die even for him. That Trevor's implied to be more surprised and hurt by Franklin's betrayal than anything else is rather heartbreaking on its own; he clearly trusted him completely.
Michael's death, as well. From Michael's distraught voice as he screams how Franklin was like a son to him, and that Michael practically let him stay at his house, to the shot of Michael's corpse on the ground and Franklin looking like he's just fighting back tears when he sees what he's done.
It's very easy to feel sorry for Debilitas, should the player not drop the chandelier onto him and opt to defeat him the old-fashioned way. Fiona feels rather guilty for killing him in self-defense, considering that Debilitas only wanted to play with her, not realizing how dangerous he was.In fact, getting the best ending requires that he survives.
There's no option that lets the player defeat Daniella without killing her, but for all her Ax-Craziness and wanting to kill Fiona, it's pretty easy to feel sorry for her when she dies. She only wanted to be complete.
Duvall, the main villain in Haze, is an extremely arrogant and over-confident jerk for the entirety of the game. When's he fatally wounded in the final duel, however, it's hard not to feel sorry for him when he's sobbing, and then begs you not to tell his mom what he's done (slicing off fingers, killing people, etc.).
Horizon Zero Dawn gives you the option to do this with Helis. If you choose the Compassionate dialogue option after defeating him for the last time, Aloy remarks sadly that for all his belief he was chosen, and the fact he killed so many, including Aloy's Parental Substitute, in the name of that belief, right up until his death he was just a pawn used by HADES who doesn't understand the forces that drive him. She allows him to look to the sun one last time before killing him quickly and cleanly, and closes her eyes sadly. It helps if you find some of his audio diaries and hear how much he loved his wife, and how devastated he was when she and his child died in childbirth. Of course, You can also take the Aggressive dialogue option...
Iji's final boss, General Tor, gets a death scene like this.
In The Journeyman Project trilogy, villain of the first game Elliot Sinclair gets this in his appearance in the third game when we find out his true motivations: he witnessed his hometown destroyed by a Cyrollan ship and spent the three and a half millennia of life granted him by exposure to an alien artifact slowly growing into a bitter old man. Having failed to stop the Cyrollans from returning, he's given up living and lost his immortality, slowly wasting away in a hospital bed in prison.
Gage: I was at Atlantis. I saw its destruction.
Sinclair: You saw it? [Heartbroken] Then you know that the most beautiful city in history was destroyed by our benevolent protectors.
Pedro Montana, from killer7, is a total bastard who sells orphans so that their organs can be used for Heaven's Smiles. But when we actually see him, he's playing handball when his partner, Curtis Blackburn (whom Pedro recently betrayed and ran out on), arrives. Pedro is terrified when he sees Curtis, and soon we discover he had a damn good reason to be - Curtis doesn't forgive. In this case, Curtis's idea of proper retribution is slaughtering Pedro's entire family... and then taunting him with stories of how they died. It's one of the hardest scenes in the game to watch, and makes it very clear that, out of all the villains in the game, Curtis Blackburn is the worst.
In Kingdom Hearts, this happens to Clayton, one of the Disney villains. While the rest of the villains willingly allied themselves to The Heartless for their own sick desires, Clayton was just a hunter who happened to be in the wrong place at the wrong time and having an emotional moment of weakness, which allowed the Heartless to find him and steal his heart, turning him into their puppet. After his death, the party expresses pity for him, with Tarzan saying that if Clayton had some friends at his side, then maybe he wouldn't have fallen to the darkness.
Tarzan: Friends, same heart. Clayton, lose heart. No heart, no see friends. No heart, no friends.
The Organization members across Chain of Memories and Kingdom Hearts II prove to be rather pitiful in their final moments as they're overcome with fear that their deaths mean the permanent end to their existence, though the emotional punch is lessened with the reveal that it actually helped restore them to their humanity once their hearts were freed from the Heartless and/or Xemnas's artificial Kingdom Hearts.
Axel dies in Kingdom Hearts II after becoming The Atoner and performing a Heroic Sacrifice to allow Sora's team access to the Organization's base. The fact that he jokes about his death makes it worse.
Sora: You're... you're fading! Axel: That's what happens when you put your whole being into an attack... not that Nobodies actually HAVE beings, right? Hehahahaha...
Saïx, despite his ruthlessness towards everyone, gets a touching sendoff as he pines for Kingdom Hearts to give him his heart back.
The Riku Replica spends his last scenes in Chain of Memories tormented by the fact that he's just a copy of Riku, leading him to try kill the original to make himself "real". Once Riku defeats him, he has this to say:
Riku Replica: So... it's over. Hmph. Death doesn't frighten me. Good riddance to a phony life. My heart was never real. I'm sure even what I'm feeling now is probably fake. Riku: What are you feeling? Riku Replica: What happens when a fake dies - one like me? Where will my heart go? Does it disappear? Riku: It'll go somewhere. Maybe to the same place as mine. Riku Replica: A faithful replica until the very end. That's... okay.
Other examples in Kingdom Hearts II:
After Sora and co. defeat the Experiment and return the presents it stole, Santa Claus speculates that it only took them because it believed the joy associated with gifts would somehow give it a heart. Dr. Finklestein backs this up by mentioning he failed to provide the Experiment with a heart during the creation process.
In the manga adaptation, Sark's reason why he works alongside the Master Control Program was because he lost faith in the users following the banishment of Ansem the Wise, and Terra-Xehanort taking his name. Since Sark had no idea on what really happened, he simply thought that Ansem betrayed him. His derezzing words were to warn Tron that Sora, Donald and Goofy would eventually betray him if he continues to believe in them. Sora, feeling sorry, reassures Tron that they will always be friends.
Vanitas in Birth by Sleep makes such a lost and sad expression as he pitifully tries reaching for the χ-blade before fading away in Birth by Sleep that it's hard not to feel some degree of sympathy for him, despite being a remorseless Humanoid Abominationmade of darkness. It doesn't help that his face is identical to Sora's, apart from the eye and hair color.
Kingdom Hearts III gives this to a number of the Real Organization XIII's members as they're defeated in the final battle, but not all:
Dark Riku (i.e. the Riku Replica from the past) is Zig-Zagged, as he's just as determined to prove he's the "real" Riku as he used to be, but gets eliminated by his present-day self, who performs a Heroic Sacrifice to give Dark Riku's vessel to Naminé.
Luxord is a Graceful Loser and gives Sora a "wild card" as a reward to help him some time in the future. The two then promise to meet up and play each other again one day, not as agents of light and darkness, but just as two everyday guys.
Terra-Xehanort averts this when he gets booted out of Terra's body by his Guardian Heartless—possessed by Terra's heart—after trying to kill Aqua and Ven.
Saïx makes amends with Axel after finally admitting his own jealousy of Roxas and Xion before dying in his friend's arms, promising to meet him again as a human.
Ansem finally acknowledges that Riku has triumphed over the power of darkness and accepts that his own time has passed, offering words of encouragement to the heroes to move on as well.
Xemnas regains his heart and suffers a Villainous BSoD, overwhelmed with a sense of loneliness after realizing he has taken all his old allies for granted, and finding new appreciation in the strength Sora and other humans have to bear it.
Master Xehanort gets a big one, where the ghost of his childhood friend/rival comes in to talk him down, remind him of better times, and travel with him to the afterlife.
Darth Malak, if you confront him on the lightside path, in Knights of the Old Republic. Despite setting up camp on the far side of the Moral Event Horizon, his doubt and regret as he's dying is just believable enough to earn a little sympathy. Bastila, too, if you decide to kill her (or have to because you can't talk her down, although less so there.)
Colonel Tobin wants to protect his home planet and goes to extreme measures to do so. His final fate, having the life slowly sucked away from him by a humanoid abomination is a grim fate for even him. You can give him the chance to redeem himself through a self sacrifice however.
Darth Sion is evil, and has very little to redeem himself with. But he is constantly in pain and only his hate and mastery of the dark side holds him together. You literally talk him into giving up, and with his last words he reflects on how empty his life was.
Atris is a fallen Jedi who's driven mad by both guilt, loneliness and surrounding herself with Sith holocroms. While their relationship is highly antagonistic through most of the game, The Exile and Atris have a lot in common and a lightside Exile might choose to bring it up and spare her.
Despite being a Consummate Liar you do get to find a lot about Kreia, and it's clear your relationship with her is very important. She doesn't necessarily want you to agree with her, though that would be appreciated, she just wants you to listen and learn from the mistakes of both the Jedi and Sith. Her final goal is to destroy The Force and given the arguments through the game you might agree with her.
The Legend of Dragoon: Greham. He was Lavitz's father's best friend, but grew envious of how strong he was, and betrayed him to his death for the power he wanted. When he falls before the party, he reveals all of this, and his last words are, "Now... I can go... to be with Servi..."
The Legend of Spyro: Dawn of the Dragon: It's revealed that the Apes were given a Fate Worse than Death by Malefor so terrible, it's rather hard not to feel some sympathy for them. They were turned into living skeletons, forever cursed to remain in the shadows and feed off the energy of others, unable to ever be full. Even Spyro and Cynder are visibly horrified by this.
Ganondorf, oddly and impossibly enough, manages to invoke a tiny bit of sympathy with his death in The Legend of Zelda: The Wind Waker. The wind is blowing indeed. In The Legend of Zelda: Twilight Princess, Link and Zelda also express pity as Ganondorf passes away, though that seems to just make him hate them all the more. His death blow is actually done by Zant, who was his servant and clearly turned on him, likely killing them both.
For most of the game he's an arrogant creep at best and deranged psycho at worst, who you learn is responsible for the murder of Rachel Amber, and when you are told that he has been murdered it seems like karma. However, Rachel's death was an accident, as Nathan kidnapped her by himself to impress Mr Jefferson, the only Parental Substitute to show any compassion or praise towards Nathan, which backfired horribly. Once you escape the Dark Room you receive his final message, a voicemail on your phone in which he warns you that Mr Jefferson is out to kill you, even as he knows that Jefferson is coming to kill him first, before he breaks down and begs forgiveness for what he's done, sobbing in remorse.
Made even more impactful if you explore his room while searching for clues and the principal's office, where you can find an email from his sister expressing concern that their abusive father (who sent her away to the other side of the world for defying him) will try to mould him into his own image to continue the family legacy whatever the cost, reminding Nathan that she still loves him and cares for him as well as the school psychiatrists report, which repeatedly emphasises Nathan's unstable mental condition. It also reveals that Nathan suffers disconnection from reality, anxiety and possibly bipolar disorder, and his psychiatrist recommends Nathan see someone more qualified for such conditions, but Nathan's father insisted that Nathan simply be given heavy medication and be left at Blackwell. Searching his locker in the locker room also turns up psych meds.
It is strongly implied that Nathan was in love, or at least infatuated with Rachel and various conversation options throughout the game reveal that Nathan's mental condition has been noticeably deteriorating ever since her disappearance/death although the only person to notice was Victoria Chase, who genuinely cares about Nathan, and her misunderstanding over this is a large part of her hostility towards Max.
Although Durandal from Marathon is not technically a villain, he is forcing people to die meaninglessly, and sends the player on suicide missions, sometimes for the hell of it. Tycho also reveals that Durandal doesn't care about humanity or the S'pht (in fact, he might hate humanity, although this may be somewhat a case of Unreliable Narrator), he just wants to find the Eleventh Clan of the S'pht because he believes that they know where he can find the Jjaro, who have the ability to help Durandal become God in the next universe. Nevertheless, he did want to stop the Pfhor invasion of Earth, and killing him was a horrible thing to do. Until we find out that he wasn't really dead.
In Mass Effect, this applies to Saren if you manage to convince him that he's been indoctrinated and become nothing more than a slave to the Reapers. He regains enough control to shoot himself in the head, letting him die as himself;
Saren: Goodbye, Shepard. Thank you.
Matriarch Benezia, as well, particularly since she started out trying to keep Saren from going too far and ended up Brainwashed and Crazy for her efforts.
In the sequel, the Collector General, when it's revealed that Harbinger has been possessing it all along. The way it looked around in confusion and reaches up at the hologram of Harbinger (because it's all it has), as the space station was blowing up around it just tears your heart out.
Although it's uncertain when, exactly, he fell, at the final moments of Mass Effect 3 you're confronted with an indoctrinated Illusive Man. He can either be made to realise this, in which case he shoots himself with a resigned, "I tried, Shepard", or he can be gunned down, following which he looks out, one last time, at the view of Earth and comments;
Illusive Man: There... Earth. I wish you could see it like I do, Shepard. It's so... perfect...
The supposed Luna VI that was actually an illicit AI called Hannibal gets one of these when you destroy the last of its mainframes. Sure, it had killed or was trying to kill everyone around it, but when you pull the plug the terminal fills with binary code that, if translated in real life, reveals the word "help" repeated over and over. Hannibal is scared of dying and is desperately shouting "Help me!" over and over as he fades away.
This is made even sadder by the revelation that Hannibal was rebuilt into EDI. She still has memories of it.
Vulcan Raven: An honorable shaman and warrior who lived a harsh life, he puts up a tough fight against Snake, dispenses some knowledge into Snake's nature, and is then eaten by his ravens, "becoming one with them."
Sniper Wolf. In between her horrible childhood and her downright painful death (including gunshots to her lungs), it's hard not to shed a tear for her.
Solidus's defeat was also somewhat pitiful on his part: He ended up killed by the Patriots via Raiden, after working hard to re-establish liberty in the USA, especially when he had nothing else to leave behind other than this. This is best demonstrated by his final actions: after falling from Federal Hall, his last visible action is him reaching up to a statue of George Washington in longing, as he attempted to redo America the way Washington originally founded it.
The Fury's dying words as he flashes back to his days in space, right before he blows himself up.
The Fury: Mission Control, do you read me? I'm coming home!
The End similarly gets a touching send off, dying doing what made him happy.
The Boss. Until a minute later, you really feel this. After that, whatever humanity there was just gets strained as you learn the truth. Considering how well it was done, it may still be a "poor villain" because of how well she played her part.
One's mileage could vary on this, but Vamp's death could count. Caught in a terrorist bombing, he was forced to drink the blood of his family in order to survive while stuck under the rubble. And with the Healing Factor-inducing nanomachines in his body, he becomes as much of a Death Seeker as Fortune was by the time Guns of the Patriots rolls around. The fact that he's smiling as the nanomachines are finally shut down in his body makes you feel bad for him. Sort of.
Vamp: I can... die...?
The kicker though, has to be every single member of the Beauty and the Beast Unit. And if their respective backstories didn't solidify their position as the biggest Woobies of the game, their death scenes, where their humanity finally shows through, are a pretty good litmus test for deciding if there is an ounce of humanity in you.
Major Zero. Sure, he was the (indirect) cause of all the events in the main series, but he truly never meant for things to go as horribly wrong as they did. By the time the AI constructs turned out to be a crapshoot, it was too late for him to fix his mistakes. When we see him at the end of the game, he's a pitiful old man - a catatonic wheelchair-bound vegetable kept alive only through life support, who can't even take responsibility for the things he didn't know he caused. And when Big Boss pulls the plug on him, the way he fidgets and spasms as his oxygen supply is cut off is downright unsettling.
Metal Gear Solid: Peace Walker: Paz Ortega Andrade (Pacifica Ocean), claimed to be a believer of peace, but was really a spy and fooled Big Boss and his people, becoming the Final Boss of the game itself. However, her dairy entries showed that during the time she regretted her actions but she felt she didn't have a choice in the matter. Fast forward to Ground Zeroes and we discover that Paz survived, but is a prisoner who was getting tortured and possibly raped for months. Chico, who deeply cared about her, tried to save her, only to be captured and used as leverage against her. In spite of all this, she found some solace and hope in having Chico, her only companion and friend in that prison camp. Big Boss is able to save her and Chico, and even remove a bomb that was implanted in her stomach. Only for her to wake up and reveal that a second bomb was planted elsewhere in her body. She sacrifices herself by jumping out of the helicopter just before the bomb detonates.
Metal Gear Solid V: The Phantom Pain: Skull Face: While he was a douchebag for most of the game, it's hard not to feel sorry for him during his final moments, slowly dying in pain after being crushed and his limbs (except his left arm) dismembered by Kaz and Big Boss, all while he begged to be killed. But then he got killed by Huey, and then he yelled "REVENGE!"
In the Mortal Kombat franchise, Mileena is a murderous Ax-Crazy psychopath who loves to kill. Thing is, when you look into her background thoroughly, you find out everything she does is for her "father", Shao Kahn, and that she just wanted to be accepted by him. In fact, Kitana's non-canon ending of 9 shows she would have made a HeelFace Turn if Kitana and Jade had simply accepted her rather than regard her as an abomination. All this makes her execution at D'Vorah's hands in X kind of sad.
This Alternate History mod provides a moment for one of the most notorious Nazis in-game and in Real Life. Reinhard Heydrich is the leader of the Waffen SS and has a somber storyline that presents him sympathetically as it goes on. He initially vomits when he learns of Himmler's plans to incinerate the entire world in a nuclear holocaust and after a few days of smoking and drinking himself into a stupor, abandoning any Spartanist ideals he once had, he scrounges up a ragtag coalition to stop the Burgundian madman. If he wins the ensuing confrontation, he realizes that his idol was an utter maniac and the fact that he had to co-operate with Polish "untermensch" who fought with valour at his side and had nothing but honesty in their dealings, Himmler's omnicidal plot and Heydrich's own association with the ideology killed more Aryans than any supposed "Jewish plot" ever could have, including one of his own sons, and alienated him from his surviving family, and the SS are in the end willing to plunge Germany in chaos again to seize power, all show Heydrich how twisted and beyond the pale Nazi ideology is. The resulting mental breakdown causes Heydrich to blow his own brains out, as he decides the world would be better off without him and Nazism. If he loses to Himmler, Heydrich is left crying out the names of his children in horror and anguish as Himmler commences his plan to destroy the world and purge it of non-Aryans.
There is a measure of sympathy to be found in the horrifically insane Sergey Taboritsky. Even as he gasses his own people and slaughters everyone with the slightest hint of impurity or disobedience in Russia until he completely kills even the idea of Russia as a nation... there is something harrowing in watching him realise how delusional and lost his cause is, becoming more insane especially after he murders his friend Nabokov. This culminates in the revelation of the obvious: that Alexei Romanov was murdered as a boy by the Bolsheviks, and is never coming back no matter what he does to "purify" Russia. He dies screaming at a horrific hallucination, pitifully begging for Alexei to return.
Nocturne: Rebirth has the Big Bad, Khaos, who wants to destroy the world and reconstruct it to the time before his friend was killed, all while believing that she's the only person who can give his life meaning. When that plan fails, he puts on a sad smile while stating he will never get a happy ending, and then commits suicide. The party is distraught by this, since they considered him a friend despite his antagonism.
No More Heroes often invokes this with the deaths of each boss, many of them being sympathetic and all of them being awesome. Good examples include Dr Peace, Holly Summers, Jeane, Ryuji, and Captain Vladimir. Alice Twilight certainly qualifies. By the time Travis meets her, she's sunk into depression, mourning the loss of Margaret Moonlight, and honestly just wanted to die. She even spells it out to Travis that the reason most of the assassins he's encountered have been so delighted to meet him is because they all just want to be freed of the endless fighting. It's also her death that causes Travis to have a What the Hell, Hero? revelation as he finally gets sick and tired of the killing.
It may seem strange that he is so obsessed with pigs, but if you read The Murkoff Account, you see that he was a Bruiser with a Soft Center who had a stuffed pig he adored. Even after he's been physically mutilated and mentally shattered, he still holds onto that piece of himself.
Eddie, clutching Waylon's hand: We could have been beautiful.
Ori and the Blind Forest has Kuro, a rampaging owl who is trying to stop your quest to revive the light of the forest at all costs. About halfway through the story, you find out the light emitted by the Spirit Tree while searching for Ori killed her babies, and she is only trying to make sure the same doesn't happen to her last unborn chick. When she sees for herself what damage she has wrought on Nibel and the immediate danger it presents to her egg, she returns Sein, the source of the Spirit Tree's life, to the tree, sacrificing herself so the forest may return to normal.
Ori and the Will of the Wisps has Shriek, the mutated owl of the petrified Silent Woods. From her birth between her petrified parents, she never found love, being rejected by other owl families due to her mutations. After Ori defeats her in the final battle, she crawls under the wings of her petrified parents to wait for death.
While Paper Mario: Sticker Star is undoubtedly the Lightest and Softest game in the series, the fourth boss, Mizzter Blizzard, was revealed to have a tragic backstory that led to him getting the Royal Sticker, which let him live like he wanted to at the cost of his sanity. He regains his sanity after losing, at which point he reveals his backstory and that he got the Royal Sticker as a result of praying to have a body that wouldn't melt. He then, in a playful manner, asks Mario to rebuild him next winter so they could play again, this time on friendly terms. To drive it all home, the narration of his backstory, which is third person for all other bosses, is in the first person here.
Persona 5: The Mole reveals that all he wanted was to be acknowledged by his father. He also admits that his goals and the Protagonists' are ultimately the same after throwing his massive tantrum, and seemingly dies protecting the party from his father's mental projection of him inside the Mental World of the Palace.
Pillars of Eternity: For most of the game, Thaos is a mysterious, yet ruthless and cruel man willing to do anything to protect the Ancient Conspiracy he founded. Then The Reveal happens and you see what he really is; a sad old man who watched everyone he ever cared about kill themselves in a mass Human Sacrifice in a misguided attempt to give the world guidance in the form of undeniably real gods. Hes spent the last two thousand years alone and miserable, manipulating society out of desperation to keep the origins of the gods secret and ensure his people didn't all die pointlessly. After he dies, your character can potentially show sympathy and understanding towards him before you decide what to do with his soul.
GLaDOS and Wheatley. Neither of them die, but during the core transfer, GLaDOS screams in pain and it's terrifying. Wheatley shoots right into antagonist territory, destroying her power. And then you transfer them again, and throw him into space, and he gets an absolutely heartbreaking apology monologue. It makes you wonder who to feel sorry for at that point.
In Project X Zone, when a villain's final defeat occurs, they may have a final speech that causes this reaction. Most notable are Aya-me and Vileof all people. This also happens to Saya again in the sequel. Even Reiji and Xiaomu express some sympathy for Saya.
Radiant Historia has a Final Boss that goes down like this. The version of his death in the Golden Ending is the most moving. The world in Radiant Historia is constantly in danger of becoming a lifeless desert, and only the voluntary Human Sacrifice of a member of the royal family of Granorg can postpone it. When it was his turn, he refused to go through with it because he didn't see anything in the world that was worth saving, and spent the game trying to make sure the only other remaining potential Sacrifice - you, his nephew - doesn't become one either. When you defeat him and make it clear that you're going to go through with it whether he likes it or not, if you've achieved 100% Completion, he decides that you are something in the world worth that's worth dying for, and performs the Heroic Sacrifice himself in your place.
Dutch van der Linde from Red Dead Redemption. According to John Marston, Dutch was once an altruistic idealist who led his gang with the goal of bettering the world. His descent into insanity was triggered by the realization that all his efforts to improve the world were futile, combined with the guilt of all his deeds. His final moments are a somber affair between him and John where Dutch shares an epiphany he's had. Dutch admits he can't change the world and he can't change his nature, so he fought all his life despite knowing it was a lost cause. Dutch ends up committing suicide rather than let himself be captured by the government he spent his life rebelling against, his death symbolically tied to the end of the romanticization surrounding the Old West.
Bill Williamson's death in I is the one that becomes more sympathetic with the addition of II. In I he's an Ax-Crazy psychopath who's the most explicitly evil member of John's former gang. Bill is revealed in II to have what seems like PTSD from his time in the army during the Indian Wars. He's also scared of getting what seems like dementia that drove his father into madness. He's also The Unfavorite in the gang despite being one of the people who's loyal to Dutch till the bitter end. Bill is also heavily implied to be gay in II living roughly a century before it was socially acceptable so he's living with a big secret (which would be hard enough on anyone, let alone someone as fragile as he is) with probably lots of shame and self-loathing tacked on for simply being who he is. It's no wonder the guy has lost it in the interim years.
Javier Escuella can count whether you decide to capture or kill him in I. He was quite a nice gentleman in II who had been starving to death in America while fleeing from his home in Mexico until Dutch took him under his wing and gave him a new life, a new home, and a new family. Javier was a guitarist and a good fisherman, often teaching Arthur Morgan how to fish; and he would often hit Micah Bell for telling him to "fuck off back to Mexico". However, his unyielding devotion to a man on the brink of collapse proved to be his downfall, and by 1911 he had returned to Mexico a jaded and amoral mercenary, working for the very government he once fought to overthrow. If John Marston decides to capture him, he is taken into custody and deported to America by Edgar Ross and the U.S. Government who would later try and hang him. On the other hand, if John decides to kill him, he will pick up Javier's corpse after shooting him down and carry him to his cell for a moment, weeping tears of sorrow that he has to bring the corpse to Ross as proof in order to claim the bounty. Either way, it's a sad state of affairs that the man who had taught Arthur to catch fish and saved John from a wolf attack is now dead.
There are two endings in Saiko No Sutoka on Normal/Hard Mode which portray the titular villain sympathetically. In the Good Ending, Saiko is impaled on glass after crawling out of a window to chase Akira. Rather than this being triumphant, it is framed tragically as Saiko is reduced to begging Akira for help. Her last moments are spent in fear of her inevitable death. In the Best Ending, Saiko is able to take back control from her alter and prevent herself from killing Akira, but it's not enough for Akira to forgive her. He runs away, and Saiko is left alone and miserable.
One of the original ones for Video Games was Oddler/Odd Eye in Shining Force II. Dude joined you as a blind kid with no memories, he follows you and clearly admires your skill, and stays behind with Creed. Unfortunately, he turns out to be a greater devil and is fought as a boss, wishing, as he died, that he could live his life again not as a devil.
Walter Sullivan of Silent Hill 4. Spends the first half of the game brutally murdering everyone the player character meets and the second half trying to kill him while laughing hysterically, but it is still almost impossible to hate someone whose final action was to desperately call for his mother. By the end of the game, the player is really finding themselves wondering if you're killing him because you hate him or if you just want to put the man out of his misery.
Skies of Arcadia gives us Ramirez's death at the end of the game. When all that's left of him is his crystal, Vyse expresses sympathy for Ramirez and requests to give him an honorable sailor's burial. Notably, he's the only real villain in the game that's shown in a truly sympathetic light, and whose circumstances are seen as a tragedy.
Invoked in-game, as part of the Retcon given to Axel Almer. Originally, in the face of death, he continued to mock Lamia and died 'being a doll on his own will'. In the remake, however, after his heartfelt confession on how the Artificial Human surpassed his very low expectations, he mutters Lemon's name before his demise, signifying his genuine care; even Raul, who was practically angry at Axel, who caused Fiona to disappear, feels bad on having to kill him. Then, it's subverted in Original Generation Gaiden, when Axel comes Back from the Dead and has a HeelFace Turn.
An even better example is Echidna Iisaki, one of Lamia's sisters. Thought to be personality-less as the W Numbers are suppose to be, in the end, she's revealed to be completely sentient when she disobeys orders to come back alive at all costs in order to take a fatal blow for her Mistress's boyfriend, Axel. When asked why, she responds that it would make her Mistress sad if Axel was killed, as, while she can be replaced as many times as needed, humans are gone when they die. Lamia begs her to eject so they can help her, but the dying Echidna defiantly proclaims "I am not... Echidna Iisaki! I... am... W16...". Axel's reaction on both occasions counts for this trope. While the original had him cursing over how a doll he hated saved his life, you feel sorry for Echidna dying and still being treated like trash by her superiors; the remake had Axel lamenting over how her death will end up demoralizing the whole Shadow Mirror army.
When Hyouma defeats Garuda in Super Robot Wars Compact 3, he tells him to eject from his mech and the Combattler team agree since he's lost the battle, he doesn't need to lose his life but Garuda says that he is content to have fought them as a real Campbellian would have, right to the end which made Chizuru asks if what he said just right now means that he isn't one. Garuda confirms it saying that it's true that he is a robot. Garuda tells Hyouma and the Combattler team that this is a battle with no hate behind them, a fair fight to the end. He only wishes that he had realized things sooner before Mia had been destroyed. Folka notes that pride alone isn't capable of changing things, he wonders what is necessary in order to break free of the cycle of tragedy. Hyouma muses that he wished that he and Garuda had met under different circumstances and Folka agrees that Garuda was a very prideful warrior even if what he believed in was incorrect.
Dark Knight Andoras in Tactics Ogre. All of 'em were jerks, sans Lans Tartare, Volaq (due to being Out of Focus, but what little we do see paint him as an honorable man), and maybe Ozma in the remakenote Only when she joins you. But then comes Andoras, who actually joins Barbas and Martym in betraying the other three, possibly for personal gain. So you'd probably think he was dislikable, like Barbas and Martym were. But he actually did it because his family and countrymen were enslaved by Lodis, and he wanted to get back at Lodis to free the countrymen he felt were "hostages". Before he dies, he even warns Denam that Valeria must be united, because that was the reason that the Bolmarkians (his nationality/ethnicity) and Nirdums (the Royal family he was a part of) fell to Lodis.
In the Gaiden Game, Rictor and Cybil come off this way. Shaher also only wanted attention from God, too.
For that matter, a lot of bosses give lines when they die, such as characters lamenting about how they couldn't give medicine to their sick daughter, how the boss was fighting for his wife, and how the wife of said boss was pregnant... Matsuno really wanted to drive home the point of how war affects everybody in terrible ways.
All of the God-Generals save Dist, who survives, in Tales of the Abyss get one of these. After the speeches they give about their ideals before their final fights (most of which involve copious amounts of angst), it really makes you feel like a douche for having to kill them. There's some Grey-and-Gray Morality in there, given some of them...
Arietta's might be the worst, however. She's one of the least malevolent of the God-Generals and has, at that point in the game, lost everything that matters to her... and unlike the other God-Generals, who mostly get fought in Boss Battles and then die off afterwards in cutscenes, she actually does die directly due to the player beating on her, her last words lamenting her failure to avenge the deaths of her mother and Ion, both of which are caused by the player party's actions. And she's only a little girl!
Sync tends to get this the least out of the other God generals (Sans Dist, since he never actually dies), mostly because he didn't seem to give as much of a shit about it all. Yeah, he's got some angst and all...but he psychologically tortures Anise and does all sorts of things that almost push on the Moral Event Horizon.
The game also does this to Grand Maestro Mohs.
On the subject of a Tales of game, Tales of Phantasia also has one of these. Which was the game's primary twist in the end, since Dhaos had stated in the very end that he didn't want to be ultimately confronted by the heroes since he was just trying to save his people. Even the characters say that they appear to be the bad guys from Dherris Karlan's point of view. Way to go, Cress.
Alice and Decus in Tales of Symphonia: Dawn of the New World. Most people despised the former after all of the cruel things she did, treating Decus like crap when he is in love with her. After their final fight, Decus even takes Emil's sword for her and died in Alice's arms. She realized that she loves Decus after all, proceeded to go into an Unstoppable Rage to avenge his death. She even cried for him. Then, she said that soon they'd be together again and held his hand as she died. This is following a few Pet the Dog moments from her, too.
Even the first Tales of Symphonia had this with either Zelos (if you got the 'bad' ending), who pulled a FaceHeel Turn (in his last words, he's talking about how his death might make life easier for his estranged sister), or Mithos himself, who started this entire 'chosen' and got involved in the 'splitting the world/harnessing mana' mess because he wanted to bring his sister back from the dead. His last words don't help.
Mithos: Farewell, my shadow, you who stand at the end of the path I chose not to follow.
Poor Walter in Tales of Legendia. He was just doing what he was conditioned to do since birth.
One really couldn't help but feel sorry for Lambda after hearing all of the stuff that was done to him by Emeraude. Almost makes you feel glad for him when he blows her up.
The same happens for the Little Queens. When the characters defeat the Fodra Queen, all that's left is one Little Queen who is still trying desperately to cling to her duty. Sophie can't help but feel sad for her.
Izebel, the Disc-One Final Boss of Tears to Tiara 2. She Is a Fallen Hero. And the only reason she did a FaceHeel Turn was because she was ordered to by her commanding officer and the person she loves in order to save their country. She had to genuinely switch sides in order guard Hispania from the worst of The Empire's excesses, and she has to bear the name of traitor and murderer of said commander as well as face the hatred of all her old friends and colleagues. Even before this, she was forced to work as a child spy for The Empire to support her sickly mother, who due to the sickness either always yells at her or doesn't recognize her. To top it all off, we learn of the truth only after Hamil ran her through with his sword.
Genbu from Tenchu 2 died on his feet and with a smile on his face. This is made all the more tragic when it turns out that Genbu is defending his boss because she was the only warrior to accept him as a Ninja, despite his otherwise comically inept ninja skills.
The Big Bad, Kagami, is an example. All she wanted to do was unite the ninja throughout Japan and free them from the survitude of abusive lords who often take advantage of them and treat them like dispoable slaves, instead of elite soldiers worthy of respect. This is the reason Tatsumaru stays with her, even after regaining his memories. And after she is assasinated, its clear that Akame and Rikumaru reasons weren't because they didn't understand her motives, but because of personal reasons of not liking her, mainly taking Tatsumaru away from them.
Lara does not feel good at all about the death of Larson in Tomb Raider: Anniversary. That they had a history together, that he really wasn't that bad of a guy, and that Lara really didn't want to pull the trigger but had no choice certainly didn't help either: she's visibly distraught after watching him die and even briefly has a brief Out, Damned Spot! moment over it. That moments earlier in the game he, unbeknownst to Lara, went out of his way to save her life by "accidentally" shoving The Kid and then missing his shot on purpose, doesn't make it any easier for the audience either.
In the middle of Trials of Mana, all the aspiring Big Bads race into the Mana Sanctuary to attempt to claim the sword of mana. However, two of them are worfed by the one who ends up becoming the Big Bad. All of them will, even if they have no connection to anyone in the party, give a sad speech about how they have lost everything and have no more reason to live.
The Darkshine Knight is no longer sustained by the Dragon Lord's power, thus when he confronts the party he informs them he has but mere moments to live, but at least he dies as himself, free from brainwashing.
Belladonna in particular - she is Driven to Suicide, and even tells Riesz (if she is present and thus not the main character) that Elliott was returned to Laurent because she has no reason to harm him.
It's worth pointing out that even on her route, Belladonna receives some of this because of her unrequited love towards her dark prince.
Thorne in TRON 2.0. Yes, he was greedy and made an exceedingly stupid mistake (that laser caused his wife to die, and his best friend to vanish - Alan Bradley is not kidding about the safety protocols!). But his PDA testifies to a lonely, frustrated life (the contact list comprises work contacts, his mother, and a shrink), and he dies horribly (being eaten alive by The Corruption).
Flowey, of all people, gets this at the end of a No Mercy Run in Undertale. After explaining how he came to be to the Fallen Child, he realizes that the Fallen Child plans to kill him, and utterly panics. He destroys Asgore's soul for you in an effort to gain your favor, then takes the appearance and Voice Grunting of his old self, Asriel, in a desperate attempt to remind the Fallen Child that he was- and still is- their best friend. The Fallen Child then proceeds to brutally murdertheir best friend. For everything he did, it's still far more horrifying than satisfying to see his demise.
Another one is Asgore. He may be the main reason that your character has to face so many monsters trying to take your soul, but he is actually a genuinely nice person. And he is killed in every ending, save for the Pacifist Run.
Maximilian. It's clear that the writers intended for him to be sympathetic in his final moments.
The Stranger who abducts Clementine in Telltale's The Walking Dead game. Before that, he was just a father trying to keep his family alive through the Zombie Apocalypse, but after losing his son while they were hunting and having all his family's supplies stolen while they were searching for him, his wife and daughter took off on their own only for him to find them as Walkers the next day. And the ones who took his family's food were your group.
Grom Hellscream in Warcraft 3. Despite slaughtering his way across two entire planets, despite embracing demonic corruption twice over, despite condemning his people, and despite frequently jeopdardising the future of the Horde...his Heroic Sacrifice and death scene in Reign of Chaos makes up for it. Almost.
The final moments of Arthas Menethil in World of Warcraft surprisingly fit this. Despite constantly hearing that nothing remains of Arthas himself, there's still enough for him to cling to his father's specter in search of some final comfort as he lies dying. Somewhat eclipsed by the ensuing Heroic Sacrifice.
Given Illidan's official Woobie status throughout much of Warcraft lore, his death (by betrayal, no less) at the end of the Black Temple raid dungeon is tragically empty. What a Senseless Waste of Human Life indeed.
Garrosh Hellscream's death in a duel against his old mentor Thrall in Warlords Of Draenor has many players feeling sorry for Garrosh, despite his well-hated status in the fandom. It doesn't help that his accusations towards Thrall aren't exactly wrong, and Thrall's refusal to acknowledge his partial responsibility for Garrosh's fate ends up making Thrall look like the bad guy.note It should be noted that Thrall decided to make amends for his part in enabling Garrosh's reign of terror by cheating in a duel so he would be forcefully demoted to the bottom of the Shaman class... which bites everyone in the ass when he can no longer lead during an even worse crisis, mirroring the way he abandoned the Horde in the first place.
"YOU made me Warchief! You LEFT ME to pick up YOUR! PIECES! YOU... FAILED... MEEEE!"
Kil'Jaeden in the Legion expansion. As he lays there dying, knowing that the heroes are going to escape his Taking You with Me attempt, he lays bare his Despair Event Horizon motivations for joining the Legion itself. Velen silently touches his forehead before teleporting out, signifying that he had forgiven Kil'jaeden's many millennia-long vendetta against both the Draenei faction and Velen himself.
Kil'Jaeden: I was always envious of you. Your gift. Your faith. Your vision. I never believed that Sargeras could be stopped. Perhaps... you will prove me wrong.
Kitaniji from The World Ends with You fits this well. He, upon realising he has failed to save Shibuya, leaves it in Neku's hands, accepting his fate for Shibuya's sake.
The final boss of Xenoblade Chronicles, Zanza, provides an odd example. In game, his death is triumphant, the end of an ageless and meaningless war, and the end of the worlds cycle or revenge, leaving few players feeling anything other than satisfaction. Come the sequel, however, and his death is recontextualised thanks to his relationship with The Architect. Turns out, Zanza is only half of Klaus, a scientist whos actions created the worlds of both Xenoblade Chronicles 1 and 2 by destroying the original. In the original, Klaus did so out of the selfish desire to be a god, but 2 reveals he also wanted to evolve humanity end the suffering of his world, which was being torn apart by war. The result split Klaus, sending half of his mind into another dimension that eventually became Zanza, with the remaining half becoming known as the Architect. While both were granted the power of a god, the Architect was left in the universe he decimated, giving him a major case of My God, What Have I Done?, leading him to try and rebuild life to atone for his crimes. After realising that the life he had created could end up just like him, he became a Death Seeker, but due to his connection to Zanza, he could only die when Shulk killed Zanza. When the final blow is dealt, the Architect is finally released from his endless suffering. In short, while in his own game Zanzas death is celebrated, with the context of the sequel it becomes a lot more tragic.
The main (human) antagonist of Xenogears vowed to use science to create a God to replace the one who had created, and then abandoned, the world. In despair over the death of his unrequited love, Sophia, he succeeded in bringing "God" back to the world in the form of a malevolent alien superweapon. Upon its destruction and his own defeat, he was taken up directly to Heaven by the true God, while telling the reincarnation of Sophia and her lover that he envies their capacity for unsullied human love.
At least half of the main antagonists in Yakuza qualifies. Yakuza has Akira Nishikiyama and Reina, who are Kiryu's best friend who turned villain, Yakuza 2 has Ryuji Goda, Yakuza 3 has Yoshitaka Mine, Yakuza 0 has Hiroki Awano and Homare Nishitani, Yakuza 6 has Takumi Someya, and finally, Ryo Aoki/Masato Arakawa and Jo Sawashiro in Yakuza: Like a Dragon.