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.
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.
The End gets a touching send off, dying doing what made him happy.
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 the USA as how the Founding Fathers founded it with liberty, 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 kicker though, has to be every single member of the Beauty and the Beast unit from Guns of the Patriots. And if their respective backstories didn't solidify their position as the official 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 the events of the series, but he truly meant well and things just went horribly wrong. 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 in Guns of the Patriots, he's a pitiful old man - a vegetable kept alive only through life support, who can't even take responsibility for the things he didn't know he caused. Eventually, Big Boss pulls the plug on him, and the way he fidgets and spasms as his oxygen supply is cut off is downright unsettling.
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.
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 Big Bad 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 Metal Gear Solid V: The Phantom Pain (Ground Zeroes, prologue) and we discover that Paz survived, but is a prisoner who was getting tortured and possibly raped for months. Big Boss is able to save her, 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 a soldier on an enemy helicopter pursuing them, detonates the bomb.
Axel from Kingdom Hearts. 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...
Even Saix gets a pretty touching sendoff. "Kingdom Hearts... where... is my heart?" Indeed, nearly all of the members of Organization XIII get touching sendoffs (eight out of thirteen, the exceptions being Xemnas, Xigbar, Xaldin, Zexion, and Marluxia), which is one reason why they get the Draco in Leather Pants treatment.
Vexen: I don't want to... go yet... Lexaeus: Forgive me, Zexion... Demyx: No waaaaaaay! *Sob!* Luxord: How could you... Roxas? Larxene: I'm... fading? No, this isn't... the way I... I won't ALLOW...!
It's been implied, though, that all of them have been reborn, and confirmed for most of them (though Xemnas is still a Big Bad and Saïx is still The Dragon).
Xemnas: I need... more rage... I need more... hearts... Sora: Xemnas. There's more to a heart than just anger or hate. It's full of all kinds of feelings. Don't you remember? Xemnas: Unfortunately... I don't.
And it's not just the Organization. A certain Artificial Human got a heartbreaking farewell...
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.
And now we have the death of Xion. As if the events leading up weren't wrenching enough, then comes the Ret Gone...
Roxas: Did I... do this to you?
Vanitas' death might be the most impressive example of this in the whole series — in spite of being made of darkness,the expression he makes right before he dies◊ is so lost and sad that it's hard not to feel bad for him. It doesn't help that his face is identical to Sora's, apart from the eye and hair color.
This actually happens to 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 even 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.
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.
The Fire Emblem series in general is quite fond of this trope. More specifically:
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.
Fire Emblem 6 has Gale, 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 Brenya 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, Go Out with a Smile included. 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.
Another is Nergal's top lieutenant, Limstella. Despite being a rather creepy, emotionlessArtificial Human, she has an absolutely gut-wrenching final moment: "I am not human. This body and this heart are constructs. Yes, as is this sorrow."
Back in Fire Emblem: Seisen no Keifu, several people Tear Jerked over Alvis, 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 Celice, whose father was murdered by Alvis, later says that Alvis does not deserve to be demonized in history.
The remake of the game adds Kleine. Throughout the game, she's depicted as a sadistic, cold-hearted killer, who constantly abuses her adoptive sister Katarina for being useless. So you look forward to the moment when you finally get to fight her...and her death comes as one of the most heart-wrenching tear jerkers in the series, specially when she asks Katarina "Stay with Me Until I Die".
Also, Eremiya from the remake. She's the one to blame for Kleine being the way she is (and Katarina, and Roro, and Roro's clones...), then when you finally beat the bitch, it's like a moment to celebra - what'sthis?! 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 Jerkass Woobie material right there. There's a very goodreason Gharnef earns more loathing than the game's actual Big Bad, Medeus.
General Zelgius (Levail as well, for that matter) in Fire Emblem: Radiant Dawn. Yes, Zelgius is the Black Knight who 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 Antivillains 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.
Optionally, Hetzel might get one. 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.
Grom Hellscream in Warcraft. 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.
Baldur's Gate's Irenicus is rather pitiable in his final moments. Even more so is Yoshimo.
Darth Malak 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.)
Only if you take the Light Side choice. If he dies in the Dark Side choice, he just mutters that you are eviler than him, and he just doesn't measure up.
Many villains in the sequel - Colonel Tobin, Darth Sion, Atris, Kreia...well, maybe not Nilhius.
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.
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.
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 in Tales of Symphonia: Dawn of the New World. Most people absolutely despised her 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 Face-Heel 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.
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 Five-Bad Band - 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.
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...
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.
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.
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.
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.
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.
The main antagonist of Xenosaga exhibits this trope as well. After commenting positively about the fact that he will no longer have to fear losing anyone (a fear which was the catalyst for his decent into psychopathy to begin with) in oblivion, he tells the protagonist, whom he has known since childhood and who is clearly distraught by the climax of their encounter: "What's with that face? You look like... you just lost your best friend." The protagonist himself is on his knees crying at this point, and you should be too. Ironically, he cries out for the antagonist not to 'leave him alone', a sentiment the antagonist exhibited in childhood upon realizing that he was immortal and would outlive the people in his life.
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 is defiantly 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. At this point with he dramatically demonstrates that you have never been free and can be (and have been) forced to do anything with the phrase "would you kindly." He is obviously disgusted by this as it contradicts everything his Objectivist philosophy is for, summed up neatly in the phrase "A man chooses, a slave obeys." At this point he "asks" you to kill him, knowing fully that you're his own son, taken from him by his worst enemy and turned into an assassin. Though Ryan's motives are famously ambiguous at times (something others comment upon in game), it seems he sacrificed himself in order illustrate the PC's fatal flaw to him, shouting "A Man chooses. A Slave Obeys" again as you beat him to death.
Songbird in Bioshock Infinite who Elizabeth is forced to kill near the end to protect Booker, by transporting herself and Booker to Rapture, and Songbird in the water where the pressure crushes him. Elizabeth comforts him through the glass of Rapture and Songbird reaches out to her, before his eyes turn from red to green, indicating a peaceful state, as he dies.
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.
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 Heel-Face 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.
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.
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.
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.
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.
Iji's final boss, General Tor, gets a death scene like this.
Doctor Breen in Half-Life 2, who genuinely believes that what he's doing is the only way that humanity can survive. His Evil Gloating and attempts at Not So Different get increasingly desperate as Gordon gets closer and closer, and right before his death, he tearfully cries "You need me!"
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 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.
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 who she had some connection to, 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 Villainous Breakdown/What The Hell, Hero moment as he finally gets sick and tired of the killing.
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...
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.
Amber and Crystal Bailey from Dead Rising 2. You only have to kill one of them to win the Boss Battle, because when you do, the other will curse Chuck for taking away her "other half", and then commit seppuku. Cliff Hudson from the first Dead Rising is also an example. 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.
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.
In Devil May Cry, after you defeat the recurring Worthy Opponent Nelo Angelo, 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 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.
The Nazis at the end of The Saboteur. As you approach their hideout in the Eiffel tower, you first assume that one of them has accidently fallen—you hear him scream and see him splat in front of you. Then, several of his comrades follow suit. The lobby is filled with dead, dying, or sobbing Nazis, one of whom drags himself towards you on his belly, choking out that, "He-he's killing everyone!" One of the soldiers plays a slow and mournful version of the game's theme, 'Feeling good', on the piano. To get to the elevator, you pass by a cluster of Nazis who hanged themselves, and at least two are play a tearful game of Russian Roulette with their pistols. Approach them, and Sean will murmur, "Keep at it mate—you'll get it right soon enough." Brrrr....
In 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.
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).
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.
Revas: You know what? It doesn't fucking matter anyway. [Looks down the shaft with an expression of fear] Just don't forget me... [Lets go]
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...
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.
The guy's long-dead when you first hear him, but Cave Johnson. Specifically, when you hear his recordings from the 1980s, and his company's nearly bankrupt and he's dying of moonrock poisoning.
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.
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.
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 dual to the death with Hawke being an intentional Suicide by Cop.
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.).
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.
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.
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.
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.
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.
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.
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 Archenemy 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.
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.