The Conquest Ending to Hyperdimension Neptunia mk2 is nothing but a string of these. In it, Nepgear has to power up a evil-slaying sword to vanquish Arfoire, which can only be done by killing off the other CPUs. You then have to fight each one and win, except Neptune who dies in a cutscene. After Ge-Ge has done all that and managed to kill Arfoire, it goes even farther by Arfoire gloating that now that there are no other CPUs, Gamindustri will stagnate and collapse, giving Arfoire the despair needed to resurrect and destroy whatever is left. If there's any consolation, it's that you get to keep the sword in your inventory if you start a New Game+.
Kingdom Hearts: 358/2 Days. Earlier in the game, the main characters talked about going to the beach on their next day off. This never happens, for a numberofreasons. At the end of the game, Roxas wakes up in Digital Twilight Town, at the beginning of Kingdom Hearts II, not remembering anything. The next cut shows him running to the Usual Spot with this line: "I hope we make it to the beach this summer!" It's sad enough for those just playing Days. It's really twisting the knife for those that have already played Kingdom Hearts II, and know what happens at the end ofthe prologue.
Also, the final boss of the game; a very sweet girl turned Tragic Monster by a Trauma Conga Line. She turns into a monster, and you have to kill her. Made worse by the fact that she gets Ret Goned right afterwards, so while you're sobbing your eyes out, none of the characters know someone who should be there...isn't... It's made even worse by the fact that Roxas forgets who she is and what had just happened while she's still dying. "Am I... the one who did this to you?" To add insult to injury, while Roxas is struggling to hold on to his memory, he takes it upon himself to remind the player that he doesn't know anything about friends other than "[those whom] I eat ice cream with." And if that's not enough, as her death scene plays out, it's revealed to ultimately be her Morton's Fork: If she doesn't die, Sora can never wake up and Xemnas wins, so she tricks Roxas into killing her, to pull her Heroic Sacrifice, while giving Roxas the motivation to turn on Xemnas. That's right, you spend a game getting attached to this girl, only to kill her so thatKingdom Hearts IIhappens.
Birth by Sleep, not to be outdone, turns the destruction of everything its three leads care for into its villains' modus operandi. The two most painful punches, however, are the murder of a weakened Master Eraqus at Master Xehanort's hand when Terra's already an emotional wreck over simply raising his blade against the man he sees as a father and Aqua's return to the Land of Departure after its destruction, carrying a comatose Ventus and remembering her failure to keep her promise to Eraqus and bring Terra back as a Master.
BBS was made even worse by Mood Whiplash when the characters happily promise to always be together... and then their voices tell you, in unison, exactly what happens next.
"That was the last night we ever spent beneath the same stars."
Goofy's apparent death in II. Sure, he comes back in the next scene, but the event comes out of nowhere and is taken incredibly seriously by everyone present, with Donald begging him to wake up before running into battle screaming and Mickey's quiet "They'll pay for this."
Sakura Wars V rolls with the Player Punches near the end. To wit: Watching Oda Nobunaga wreck New York City after having spent every mission up to that point saving it, having player character Shinjiro nearly killed by Nobunaga, discovering that the only way to defeat Nobunaga would require your love interest to sacrifice her life...
Lucien, Big Bad of Fable II goes out above and beyond the call of this trope. In order: first he kills your sister (your only family) in front of you, immediately afterwards he shoots and very nearly kills you, a decade later he enslaves you as a guard (with regular torture, of course) for ten years as a young adult, then he takes all of your allies after you escape, personally kills your spouse and children, and just to top it off he kills your faithful dog. All of this alongside his various other atrocities. At some points it seems like the bastard spends his free time looking for new ways to piss you off.
Phantasy Star II had Nei, the cute little biomonster-human hybrid that the protagonist has adopted as his surrogate little sister. About halfway through the game, we encounter her prototype: the brutal Neifirst who quickly disposes of her "little sister." Cue the boss music!
In Phantasy Star IV, players shouldn't really get attached to anyone in the last slot in their party, because they have an average life expectancy of less than an hour for the middle part of the game. Even if they don't die, they generally leave the party almost as soon as they've joined.
On top of that, Alys' death was just plain undignified. She got hit with an extremely virulent attack, and spent a week dying in bed with the characters visiting her regularly. The initial punch came with the infection, then was just drawn out rather than the usual 'stab-dead-wait what?'
The worst part is that the story arc that comes right after Alys' wound is a desperate chase after Rune, the most competent sorcerer of The Verse. So what happens? They find a vehicle to reach the region where he is, find the guy, bring him back to Alys, and what does he say? "Nope, that's beyond my expertise, she's going to die." Yeah. The last two dungeons, and the Hope Spot when you finally found the guy? All for nothing.
The second-worst part, although lessened because it's several hours of gameplay later: the disease Alys died of? It's not even unique to her. There's an entire town full of people who died of it and eventually rose from the dead as zombies, a hospital full of people who are dying of it when you get there, and there's still no cure but rooting out the evil that's spreading it. Alys died no differently from an entire town of nameless, faceless NPCs.
In Final Fantasy II, your party has a rotating fourth slot for guest characters — almost all of whom die. Even when they don't, you're usually left to think so for a while. Few moments from the NES era are as depressing as when Josef's little daughter realizes her daddy won't be coming home.
Also, while it's less personal than losing a party member, the Dreadnought's destruction of several towns you've visited is a tough pill to swallow. What's worse, you don't see it happen — you just see the murderous airship take off, and then the next time you enter a town, it's in ruins. You can even talk to the few survivors, including at least one newly orphaned child. Before this event, the player probably dismissed the Emperor as a generic RPG villain. No more.
Even worse is the aftermath of the Cyclone. All of those towns become nothing more than greyish patches of ruin on the map. You can't even enter them anymore to talk to the broken survivors because there aren't any. What's more, this leaves only Fynn and a few distant places like Salamand and Mysidia standing. The Emperor has now managed to destroy most of human civilization.
Final Fantasy III's Kraken would be unremarkable were it not for his cold-blooded killing of your guide, who's a defenseless maiden. The only bright side is that this comes before the fight — allowing you to take full payment out of Kraken's briny hide.
In actuality, he was aiming for your party leader. The maiden pushes him out of the way and gets hit. So, her death doubles as a player punch and Heroic Sacrifice.
Meanwhile, Final Fantasy IV gives us plenty of Player Punch fodder, and actually does so on a gradually increasing "caring" scale. For instance, one believes, unless he/she has read about the game online, that Rydia, who the player has from almost the beginning, is lost when the ship is attacked by Leviathan (who technically isn't a baddie). Later, after a fight with the second Elemental Fiend, Porom and Palom, bite it. Later, you get back Tellah, who now knows almost every spell in the game, and not even half way through the story, who naturally gets his own later fighting Golbez. A bit later Yang saves the Dwarf Kingdom from a giant cannon by stuffing his body into the barrel, and minutes later the quirky engineer Cid blows himself up to block a pursuing enemy force. Then there's Edge and his parents.
Of course, the Rydia thing is spoiled by opening the game itself in the Nintendo DS remake; if you watch carefully you will see Adult Rydia appear several times, even summoning Mist Dragon, thus forgoing any suspicion she might really be dead.
Earlier on, Final Fantasy V had Syldra - Faris's best (perhaps only) friend through most of the pirate's life, who's briefly introduced to the party by hilariously scaring the crap out of them. Then comes the boss of the Walse Canal...and much later in the first world, when you've thought Syldra dead and gone, she returns to save the whole party from the Walse Tower, at the cost of her own life. The cry after the screen fades to black is truly heartbreaking. Thankfully, once Exdeath remerges the worlds, she is resurrected as a Summon.
After Exdeath merges the worlds, he gains the power of the Void and uses it with reckless abandon. His first target? Castle Tycoon—where he apparently kills Lenna. Fortunately, her wind drake saves her...! at the cost of its own life. And later, Exdeath attacks Bartz's hometown, the Moogle Forest, the Ancient Library, and several other places just to be a dick, which makes kind and easygoing Bartz snap. Oh, and just before the Very Definitely Final Dungeon, Exdeath goes after even more places, including Krile and Galuf's kingdom.
Final Fantasy VI had General Leo, who, despite being on the other side, was an incredibly sympathetic character, particularly in contrast to Kefka. Probably doesn't help that the game lets you play as him in all his overpowered glory defending innocent people right before his death. Kefka was a bad guy before (he long-since crossed the Moral Event Horizon after the poisoning of Doma,) but damned if that didn't hammer it in.
To be honest, the first half of the game exists only to establish Kefka as the worst villain possible. See: the enslavement of Terra, the attack on Figaro, the poisoning of Doma, the attack on Narshe, the scenes in the Magitek Research Facility, the murder of Leo and all the Espers, the murder of Gestahl and the sundering of the world.
The death of Cid, assuming you let him die, which hits especially hard when you find out in some guide somewhere that it's your fault for feeding the sick old man whatever lousy fish you could get your hands on. He had just adopted Celes as his granddaughter, you jerk! But many players think that it is better for Cid to die because of the poignant attempted suicide that follows as well as being better character development for Celes.
One of the recurring themes in Final Fantasy VI is dealing with the tragic death of a loved one (and thus many Player Punches, even characters killed in flashbacks). Locke is hurt when he didn't get to hear how Rachel felt about him when she died (she was killed in an Imperial attack). The murder of Cyan's family (during the poisoning of Doma) would haunt him throughout the game, leading to his nightmare in the World of Ruin. Gau is literally thrown out into the world alone, shunned by his own father and forced to fend for himself until he finding his true family within the heroes. Setzer loses his friend Daryl, but finds hope in her airship. The death of Sabin and Edgar's father (due to Imperial poison) would test them as brothers. Terra loses her "guide" when Leo is killed. Cid expends all his energy caring for Celes and if he dies, Celes doesn't realize what he done for her until after her suicide attempt fails. Some characters never get over their loss, Shadow for example. While Final Fantasy VII may have one of the most famous character kills of all time, Final Fantasy VI goes deeper into the theme of tragic loss.
There is also a town of orphaned children, and post-sundering, virtually everyone you meet has lost a loved one.
There's a secret bonus "mission" where Sabin and Cyan (the two Gau has imprinted on) find Gau's father. They groom Gau, teach him to act more human, and prepare him to be reunited with his lost family. Only to find that Gau's father casually refers to Gau as a monster that killed his wife, in front of Gau!
To this day the first sticky on any FFVII forum has to be titled "no you can't revive Aerith". This was made worse by the fact that you could see shops selling upgrades to Aerith's staff all the way to the end. Apparently this was done to punch the players some more but everyone took it to mean there must have been some way for Aerith to survive...
Ten years later, they managed to repeat this with a game that is essentially a massive Player Punch just waiting to strike with Crisis Core. Every Final Fantasy VII fan already knows what is going to happen, but it still counts a Tear Jerker for a number of people who played it. The fact that Zack's death scene is meant to be complimentary to Aerith's only made it more poignant.
The Modeoheim mission in Crisis Core where Zack is forced to do in his mentor, sometimes considered father-figure, Angeal And later the scene/cutscene where he confronts Sephiroth, who has become one of his dear friends and gets soundly thrashed only watch then watch this same best-friend-gone-beserk shishkebab his "adopted" little trooper.
Remember the people in the slums? The innocents that you've been drawn to, that you're fighting for? Remember Sector 7?
Speaking of Sector 7...Avalanche members Biggs, Wedge, and Jesse. You spend a great deal of time fighting alongside them, arguing with them, cracking jokes with them, really coming to love them like family...and then they get slaughtered just before that entire chunk of Midgar is dropped on top of their remains.
In Final Fantasy VIII you have the first visit to Selphie's hometown of Trabia, which is full of sick and injured people, and a lot of them have passed on, and are buried in the graveyard. It gets really bad if you you have Siren's Move-Find ability and go to the graveyard after Selphie stops praying there and find the hidden draw point Zombie magic which really adds salt to the wound.
Also Odin's fate if you find and recruit him before fighting Seifer in Lunatic Pandora. Let's just say Seifer is going down hard.
This occurs in Final Fantasy IX to the mindless Black Mages, who resemble the main character Vivi, aboard an airship early in the game. They end up getting systematically annihilated by a boss, much to Vivi's horror, after they try to protect the party.
Final Fantasy X has Luzzu and Gatta, whom you encounter frequently throughout the early points of the game and observe their actions as they follow the doomed military organization, The Crusaders. Eventually one of them (whom you can choose) dies in a horrifically failed attack on near Cosmic Horror Sin. Just to rub it in, afterwards you can have another encounter with the survivor, who is invariably torn up with grief, horror, and guilt.
Later in the game, when it's revealed to Tidus that performing the Final Summoning to defeat Sin (which has been Yuna's goal since long before her introduction) will kill the summoner. Made even more of a Player Punch by Tidus's extremely emotional reaction as he laments all the things he said to Yuna that now seem extremely cruel, considering she'd be dead (like offering to return with her to certain places after beating Sin).
The entire population of Ronso (with the exceptions of the Blitzball team and Kimahri) are slaughtered by Seymour in a subverted You Shall Not Pass moment, which thankfully occurs offscreen. The Al Bhed suffer a similar fate, but not to quite the same extent, at the hands of the Guado, but you actually have to walk through their burning home.
Final Fantasy X-2, the sequel, has a particularly nasty one. There is one mission in Chapter 3 which may be difficult depending on answers to questions in the previous two chapters. The mission is not essential to continue the story, and you can get an accessory for skipping it - but the boss you didn't fight will commit genocide on the Guado.
In Final Fantasy Crystal Chronicles: Crystal Bearers, there are plenty of NPCs to interact with but only between six and nine real characters. Of the three female characters, Belle is a greedy, whiny, ungrateful backstabber (though she gets better by the end), Altea doesn't really interact with the player character that often for most of the game, and Amidatelion/Goldenrod is the one the player spends time chasing around as an enemy only to find out that her reasons for putting people in danger were more sound than they initially seemed (though the player may or may not agree with her actions at the point) and that she wants you to come over to her side. Plus, her VA was way more interesting and less annoying than Belle's. So it's not easy when Jegran kills her by turning her to crystal and the player character holds her in his arms while she dies telling him how helpful he's been and how much she's learned from him.
In Baldur's Gate II, Big Bad Jon Irenicus establishes his evil credentials in the opening sequence by torturing and kidnapping the PC's childhood friend, fan favorite and Loveable Rogue Imoen. Originally, the developers planned on having you arrive to rescue her only to find her driven insane by the tortures inflicted on her. Fan outcry was so great that the game was altered so that she got better.
Khalid and Dynaheir, however, were not so lucky; both got tortured and killed by Irenicus and their bodies mutilated (although neither were as well-characterized as Imoen). Also, there was that whole Yoshimo business in Spellhold, which worked just as well as perma-insane Imoen would have in making one hate Irenicus' guts. Especially as you have to cut out his heart to keep him from going to hell for all eternity.
In the original Baldur's Gate, having to fight the doppelgangers of the people of Candlekeep.
Speaking of inanimate object "death," Grodus from Paper Mario: The Thousand-Year Door ups the antipathy by deleting TEC-XX's files as the computer sends Peach's last (incomplete) message and tells her in a text scroll that he loves her.
In terms of player punch inducing villainy, Dimentio's revelation of just how psychotic he is by attempting to kill the defenseless Bleck, then laughing about it when his shot hits Nastasia instead.
Not to mention having to essentially fight Luigi as the Final Boss, after he's been brainwashed and consumed by the power of the Chaos Heart by Dimentio. He recovers, but damn, that's harsh.
Or the young Squirps. Sure, he's basically like an annoying little kid for the entire level, but then you get to the very end of it, and dear god, the poor little kid is all alone.
What about Sammer's Kingdom? Fight your way through a tournament full of enemies, only to lose the race against time. You come back to the world to find the colorful landscape reduced to a white background and a few crumbled line drawings, and the Pure Heart is inert.
The fan-made module The Bastard Of Kosigan has a couple in the second chapter, at least for good players. Alex's death and the brutal murder of both of your cousins, the older one's family, and your uncle are pretty bad.
The first chapter of the fan-made module A Dance with Rogues feels like it is designed to throw these at you in succession, spaced just widely enough apart that you get hit by one immediately after you get over the last one. It starts with your family's death in the prologue, followed by some time for your character to adjust to her new life and start picking up the pieces, and then your good friend Caron is slaughtered by the Dhorn, followed by a few more adventures to give you a chance to get over it, and thenthe Dhorn find and capture the entire leadership of Master Nathan's group, starting you on the mission that forms the core of the second chapter.
Adam Miller's NWN Shadowlords/Dreamcatcher/Demon campaigns pull off a rather unique instance of the trope. In the first model of Dreamcatcher, your NPC partner (who has stuck with you since the beginning of the Shadowlords campaign, and who you have quite likely romanced or become very good friends with) begins to act strangely. Around this time you encounter some Doppelgangers. Enough dialogue will reveal that your partner has been replaced by a Doppelgänger, which then attacks you - and when you kill it, your partner is still missing. Cue bloody rampage until you find him/her.
In Neverwinter Nights 2, this occurs when Shandra Jerro suffers a Plotline Death at the hands of her own grandfather. This is not so much upsetting because the player has developed affection for the character, but because she is replaced by the aforementioned grandfather, a warlock, thereby shifting the melee/magic balance of your party.
And as he comes in late in the game, you don't get to spec him to your liking, and he turns out to be fairly useless. Most frustratingly, there are two cases in which he's a required party member, one of them at the very end of the game.
Fortunately, he had a much better personality than Shandra (who many players despised) and was possibly one of the most enjoyable party members in the game.
After indirectly destroying Shandra's farm and endangering her life, she joins your party, where she becomes your squire and learns the life of a hero. Spending weeks training (okay, this was off-screen) and encouraging her, helping to save each other and her effectively being a mirror to you and your life, she gets killed because of several misunderstandings by her grandfather. Who joins you afterwards. Ouch. Luckily, he's more likable than it initially seems.
In Contact it turns out that the companion who's betrayed Terry (the main character) is the player him/herself. Possibly serves as a subversion; Terry doesn't betray the player, he just gets fed up and attacks you out of frustration after the game's Shaggy Dog Ending. It's not a fight to the death - you tussle until he collapses exhausted, then he says Screw This, I'm Outta Here!.
Required Super Robot Wars reference: in the Original Generation games, we meet the Colonel Badass Daitetsu. He's old, but experienced, a father-figure for his crew, and one of the few people that can keep up with Hard-Drinking Party Girl Excellen. Over the course of the two games he's in, he manages to survive a hopeless battle against the Aerogators in the back story and escape back to Earth, the Kurogane drilling a hole through his ship, Gaza nearly destroying the ship, taking on several Sealed Evil in a Can entities, and encouraging his XO Tetsuya to grow and become a captain as well. Three quarters of OG 2, Lee Linjun hits his Moral Event Horizon by firing on Daitetsu's ship in a way that kills the man. The crew is devastated, and Elzam sheds his Paper-Thin Disguise for the funeral because maintaining it would be an insult to Daitetsu's honor. Tetsuya gets his revenge when he uses the Kurogane to cut through Lee's ship at the end of the game. This final moment is poignant and emotional.
Hey at least we may see Lee gets an even worse punishment, should he even show his face to you again.
There are plenty of other Player Punches in SRW, but most are spoiled by knowledge of the shows involved, and the fact that generally a fan favourite will be savable.
Here's one more involving the Originals: Poor Toby Watson in Super Robot Wars Z is a member of the Glory Star along with heroine Setsuko Ohara and his superior Denzel Hammer. He's separated with Setsuko after Asakim murders Denzel. For some reason, he manages to reunite with Setsuko after much hardships. And then they meet Asakim again... who proceeds to kill him in front of Setsuko. That alone cements Asakim as the monster amongst the original characters.
Setsuko herself. Denzel was a father to her, Asakim kills him due to an unfortunate bit of irony (Denzel switched mechs with Setsuko that stage and Asakim was gunning for her). Break the World sends her away from Toby and has her lose her memories. She gets better, only to have Toby get shot down and Rand want to kill her due to a misunderstanding. One retrofit later, Toby comes back, only to shoot her down this time. Surprise, surprise, it's Asakim. He proceeds to describe how her suffering is the only way that he can die, for she is something of a Barrier Maiden for parallel universes and her despair weakens the connection. While brutalizing (and possibly raping) her. Then her alternate dimension comrades try to kill her because of misinformation from the true Big Bad. Finally, it's possible to lose her route; at which point she loses her sight, smell, and hearing before dying in absolute despair. Isn't it sad, Secchin?
MX has among the most sadistic Player Punch ever Rahxephon has just averted the Bardiel incident from Evangelion, saving Touji. The tradeoff? This stage also has the same part where Ayato accidentally kills Asahina because she was synced with the Dolem Ayato was fighting. Think those guys at Banpresto would have a way to avert this sequence like so many other times? That we'd be saved a Tear JerkerKill the Cutie and we'd have warm fuzzies seeing her live? Fucking hell no. What's worse, not only does Ayato still kill Asahina, this sequence is done with the player in control. That's right. You have to make Ayato do the deed. Needless to say, anyone who can't stand being forced to Kill the Cutie / The Woobie is in for a kick in the balls.
Super Robot Wars Alpha 2 First, The CutieToken Mini-Moe Irui turn out to be the Big Bad. At least you got to choose either to kill her or try convincing her back. Choose latter and her alter ego takeover and become True Final Boss. When you finally defeat it, only two of protagonists can save her from exploding Physical God. The worst got to be Ibis's events. As our heroine tries to rescue her, Irui knows that Ibis's Fragile Speedster mech won't make it. So she used her last strength pushing Ibis away. At least the last game made it clear that she survives.
Any seasoned player of the Tales Series of games would know to expect one. The first of such punches came in the very first Tales game of the series: Tales of Phantasia, where one of the things you first have to do in town before leaving to hunt boars is to deliver an apple to Chester's sister, who's such a sweetie. She doesn't survive when town gets leveled.
This is one of the earlier things presented in Tales of Destiny 2. Prequel hero Stahn Aileron is believed to be 'on a journey, and haven't come back'... but later we found out that before the game timeline, the game's The Dragon had him Killed Off for Real, and his son, the game's hero, was just in delusion about his dad's travels. Maybe Stahn was the hero of the first game, but he's more or less a supporting figure in the second game, where he was killed. (In a subversion, after this, instead of being thoroughly hated, said Dragon EXPLODED into a fan favorite villain.WOW)
Another is presented in the end of the game, after beating the final boss, time is fixed, and events such as Stahn dying is annulled. But this also annulled the revival of one of your party member Judas, a.k.a Leon Magnus, since he was supposed to be revived by the Big Bad. Which means, yes. He's dead again and never coming back, and his deeds of saving the world will be forgotten and he's still marked as a traitor in history.
Then, once you've gotten your vengeance on Remiel, Kratos appears in a new outfit, and Remiel begs him for help. Kratos confirms Remiel's statement that he is one of the Four Seraphim and Remiel's boss, then just lets the angel die before fighting you. Kratos' betrayel is especially bad if you've gotten all the optional cut scenes with him, because it shows him bonding with Lloyd over the journey. It gets even worse when you discover that Kratos is Lloyd's father
Fortunately, there's an optional scene which shows that Corrine comes back as Verius, the Summon Spirit of Heart in the Martel Temple. Unfortunately, you can't actually summon him.
Hell, the second boss battle is a major Player Punch. The battle starts with the evil army invading and razing Lloyd's town and setting a monster on him and Genis. After you win, you find out that the monster is Marble, an old woman Genis had befriended. Even worse, the commander implies that she was turned into a monster because of her association with Genis and Lloyd.
Additionally, if you play the game a certain way and take too much effort to patch things up with an errant teammate Kratos, you end up facing Zelos, the vain Chosen One who's known all along that he was going to die a martyr and has quietly resented it his entire life. Zelos picks up on the values dissonance coming from the hero and decides to serve up some of his own. In this case, you kill him for real and never get to truly understand his side of things, while the other way everyone gets by happily and you have a chance to learn his motivations. He even jokes about his hatred with his usual feigned carelessness.
This one is actually twice as bad if you play it the other way first, and pay close attention to dialogue changes. If you choose to keep Zelos around, Lloyd will declare that he trusts Zelos as the party leaves Flanoir - most players agree that this is what prompts his Heel-Face Turn. Pick Kratos, and Lloyd will instead doubtfully ask Zelos if he can trust him. Zelos insists you can, smiling as usual. And no matter what option you pick, in a skit that appears just after his death or betrayal, Sheena and Lloyd lament that they didn't pay more attention to Zelos, who has basically been both Stepford Smiler and Butt Monkey since your arrival in Tethe'alla. You, Lloyd and the rest of the party have worked together to alienate Zelos to the point where he refuses your friendship and basically commits Suicide by Cop. You Bastard.
Arguably later in the game as well, when every single character who isn't Loyd in your party pulls a Heroic Sacrifice to allow Lloyd to reach Colette, Mithos/Yggdrasil and Pronyma. Granted it turns out they all managed to live somehow and as such it doesn't sting as bad, hence its arguability.
When the Big Bad tricks Luke into destroying the mining town Akzeriuth, thus dropping it into the Qliphoth—a bubbling sea of toxic, boiling hot liquid mud—that's hard enough. But the scene afterwards, when the party is recuperating and a little boy is adrift in the mud...no matter how hard you try, you cannot save him, all you can do is listen to his agonized screams as he slowly sinks to his death. Probably one of the most horrifying scenes in an RPG.
Less horrifying but no less striking is the death of General Frings, the Mauve ShirtReasonable Authority Figure of Malkuth's army, which kicks off the new plot developments after the month-long timeskip and shows that the world isn't as saved as you thought it was. Particularly painful if you went through the long sidequest sequence getting him and General Cecille together, and watched the character skits about how their romance was a symbol of hope for their two nations to finally get along...
Mass Effect 1 delivers the metaphorical kick in the balls when Shepard is forced to leave behind either Ashley or Kaidan to die in a massive nuclear explosion, made worse by the fact that you have to choose which one kicks the bucket. Not to mention that, depending on your gender the one you kill may be your lover! And if you spare your lover, they will wonder if that's the reason. The only way out of this is to pursue Liara as a romantic interest instead.
Yet another choice during the same mission can be counted as an indirect Player Punch. Fan favorite Proud Warrior Race Guy Urdnot Wrex becomes incredibly angry and conflicted when he learns that Big Bad Saren had found a cure for the sterility plague affecting the Krogan... and that you will have to destroy it in order to defeat Saren. If your Charm or Intimidate scores aren't high enough, you will either have to Shoot the Dog or Ashley will do it for you.
It begins with a player punch, specifically the destruction of the Normandy and the death of many of the named background characters, including your carefully hand-crafted Commander Shepard him/herself.
The deaths of any of your squadmates during the Suicide Mission. No matter who dies, you are going to feel it, either because the game goes a long way to characterize each one of them through Recruitment and Loyalty missions, or if only because you know that the only reason that squadmate died was because of your actions. You could have saved him or her, and their death is on you and you alone.
Be advised to put off getting that Reaper IFF until you're ready for the endgame. Sure, you can continue jetting around for as long as you like... provided you don't mind letting your ship's crew get ground up into bloody mush to fuel a fetal Reaper, one of them right before your eyes, screaming as she's melted. Even Cool Old Lady Dr. Chakwas, the only one left, gives you a What the Hell, Hero? for having let it happen. Even if you do head straight for the endgame after that scene, the only difference it makes for that scene is that the person being liquefied is a colonist from Horizon instead of Kelly.
Liara's reason for wanting to kill the Shadow Broker will probably make you want him/her/it/them dead as well.
Horizon is one hell of a Player Punch, especially if you spared your non-Liara love interest in ME1.
Early on in the game you are sent to recruit Archangel, a vigilante that has caused three rival mercenary factions to form a truce to kill him. You get there and find out that the crusader is none other than Garrus. Who promptly takes a rocket to the face. While this is shocking, he soon recovers, but is left with huge scarring on his face. You can later find a transcript of a conversation with his sister, who is pissed because he no longer video chats with them, implying he is ashamed of what he looks like now.
In the Overlord DLC, we get treated to the pleasant discovery a doctor who has wired his autistic brother to a machine in order to create a human VI. And you get to decide whether or not it stops.
Mass Effect 3 puts both of its predecessors to shame, being more of a Player Curb-Stomp Battle. Not least because it starts out with Earth being the target of a No-Holds-Barred Beatdown by the invading Reapers so hard that the explosions can be seen from space, and it only gets worse from there. Depending on previouschoices made in 1 and 2, it can be filled with these. Even if you did everything right, the list of punches it doles out guarantees at least a few cracked ribs by the end.
Special mention goes to the Thessia mission. First, the critical data you were sent to retrieve is snatched from right in front of you by Kai Leng. Then, as he's flying away, Shepard watches helplessly as the last of the resistance on Thessia is crushed by the Reapers. Then, you get to explain to the asari councilor that because your mission failed, her homeworld is pretty much doomed. Shepard even undergoes a brief Heroic BSOD, a Mass Effect first.
The Tuchanka mission earlier in the game. After being given a deal by the Salarian Dalatrass to fake the Genophage cure in exchange for salarian war assets, Wrex and Eve procede to preemptively guilt trip you throughout the entire mission. At the end, you have to choose between shooting Mordin and gaining salarian support or letting him go, apparently losing any chance of salarian help and unleashing the krogan on the galaxy once more. As a bonus, Mordin dies anyway, and if you chose to fake the cure, you later have to shoot Wrex and get called out on it by Garrus.
The third option is to save Captain Kirrahe in the first game, so that he can get you salarian support if you end the Genophage. That's it. Either you kill Wrex in the first game, lie to him and kill him later, or Mordin dies by your hand or saving the krogans from extinction.
And of course, there's Rannoch. At the end of the arc, you get the choice between allowing the geth to upgrade and blast the Migrant Fleet out of the sky, or stopping the upload and letting the quarians destroy the geth. Unless you jump through a very specific series of hoops, you're going to have to choose between one of your two teammates. And even if you do get the good ending, Legion has to disseminate its runtimes among the geth to finish upgrading them.
If you can't get the third option, be prepared to bawl your eyes out either way; if you choose the quarians, Legion will attack you in the desperate hopes of making you help his people, and you have to kill him. Then his race is completely obliterated for something the quarians forced them to do, and you get to listen to them be smug about it afterwards. If you choose the geth, Legion still dies, you watch the quarians be blown out of the sky because their Jerkass commander wouldn't let them retreat, and right after that, your sweet little-sis-figure/love interest Tali commits suicide, and there is absolutely nothing you can do to stop it. It does not matter if you are Paragon or Renegade. It does not matter if you romanced her. That Paragon interrupt does nothing. Youwillwatch her jump off that cliff no matter what.
If you didn't recruit Legion in the second game, you're forced to fight him at the Cerberus base, brainwashed into one of their units. Worse is the fact that while this hurts the player, none of the main characters care at all.
Even worse, if you did recruit Legion, but he died on the Collector base, you get a Legion replacement. Who has no recollection of anything to do with you. While Legion cared for the crew and trusted them, the new Legion doesn't, which really hits home how much of an influence you had on Legion. When you side with the quarians (as there is no longer a third option) he rants that he knew he shouldn't trust organics, whereas Legion tries to reason with you before becoming desperate.
This is also the point you (the player) realize that there is no way to save Legion, who you will have almost certainly grown to love. He is guaranteed to die in this game, an honor that only one other party member, Thane, gets.
If you don't go to the Academy, it will eventually stop showing up on your map, implying that Cerberus succeeded in taking over. The real Player Punch, however, comes when you assault their base; if Jack survived the last game, you find that she was recaptured by her worst enemy, indoctrinated, and turned into a Phantom. Which you are then forced to kill. You can also find an audiofile of Cerberus torturing and Mind Raping her. Bioware really went all-out with the guilt trips.
Similarly, if you delay in going to disarm a bomb on Tuchanka, it detonates. A large portion of the krogan population, possibly including Eve, is killed. Shortly afterwards, the clan leader sends you an e-mail expressing rage (Wreav) or weary shock (Wrex). All because you didn't disarm a bomb despite all the warnings.
While many of the previous punches are good, one that was less well-received among the players was the heavy-handed inclusion of a little boy during the prologue on Earth. His death and its impact on Shepard is constantly played on, which some players viewed as attempting too hard to establish an emotional connection.
The Legend of Dragoon has a good Player Punch with the death of Lavitz, who charges Lloyd as a Dragoon when he takes the Moon Gem from King Albert, only to get skewered by the Dragon Buster (a sword that's pretty much lethal to anything dragon-like, including Dragoons, who actually USE the power of dragons, remember), killing him off in a rather sad scene which ultimately fuels the player's resolve to defeat Lloyd.
It doesn't help that you've spent plenty of time getting to know Lavitz; he saves Dart's life on multiple occasions and is generally a great person and friend to Dart. You even visit his mother's house, learn how he's a momma's boy at heart, and he discusses his childhood and motivations with Dart.
Vampire: The Masquerade – Bloodlines has Heather Poe, whose life you save out of pity at the beginning of the game by turning her into your ghoul, a personal blood-addicted slave for whom your blood is like your home and your love and affection. She even drops out of college to spend her time with you and brighten up your bleak unlife. She is the closest thing you have to a friend, being truly grateful to you for saving her life and never trying to manipulate you like others do... AND THEN THOSE SABBATH DREGS KILL HER!!! This is made worse by the fact that if you had the willpower to send Heather away before the final chapters, she would have survived the story and eventually gotten over her addiction to you. You also get a Humanity reward for doing this...
Another Player Punch during The Sabbat Raid with blood splatters where Chunk should be. He survives, but it's still one more reason to hate the Sabbat.
It's hard to think of a game with a Karma Meter that results in such a wildly diverging ending as Jade Empire.
While the endings come from a mix of Karma Meter, Sanity Meter, and player choices, Geneforge gives you endings ranging from becoming an absolute despot of all you behold to fleeing with your tail between your legs to getting executed ignominiously. And yes, these are all possible victories, not just nonstandard game overs.
Mega Man Legends 2 had one of these with a not-quite death: During a boss battle on top of an airship, the boss you're fighting shoots down the Bonnes' escape pod, annoyed that they're cheering for you.
Enchanted Arms must have read the design document for God of War, because you're forced to kill your dog who has been turned into a Cerberus. The worst part is that afterwards, you can resurrect the dog... As a completely emotionless automaton. And if you want 100% game completion, you HAVE to commit this atrocious act.
A slight correction: Golems are automatons, yes, but they are not mindless. Aside from the Devil Golems, Hanako (the kunoichi Golem in Kyoto) clearly had genuine feelings for that perverted lord of hers, even if the target of her affections was questionable. Similarly, the Divine Beast Golems are perfectly sentient and the canine Golems early in Yokohama are stated to act like real dogs, including getting attached to humans. Golems appear to be emotionless because the presence of Devil Golems made them go rampant again, but most are sentient enough to be pets, and some are smarter than that.
Breath of Fire I opened with Sara, the hero's sister, singlehandedly confronting Jade to stall for time so the rest of the hiding villagers aren't discovered, losing, and being led away. Later, you find her and think you've rescued her, but she betrays you and runs off with the Goddess Keys you had been collecting. Later still, you confront her in Jade's fortress, where she reveals she's been placed under Jade's Mind Control and has been slipping in and out of his control, slips back under control just after saying this, fights you, finally breaks free just after the fight, and dies. Finally, when you confront Jade, he mockingly asks what took you so long to reach him, saying he expected you to get through Sara faster than that. It was at this point that you decided that Jade must die, questions of who's the true Big Bad and who's the Man Behind the Man be damned.
Also in the original, the quest for the Time Key is heartbreaking. You finally convince Cerl (one of the villains) to give you the key by bringing her fruit that reminds her of happier times with an old friend (Alan). One of other villains appears and she holds him off while your party escapes. This takes place in a castle that reflects her mind. Just as you escape, Alan runs into the castle to save her. Then the castle (and everyone in it) disappears. If you return to the site later, you see ghosts of Cerl and Alan playing as children while hearing one of the most tear-jerking songs ever found in a game.
Unless you interpret the scene as being another timewarp, with Alan and Cerl being reduced to children again by the effects of the Time Key. Then it becomes far more optimistic, giving the pair a second chance at happiness.
Breath of Fire II wasn't much better, with a raid on the evil church's Vatican-like headquarters claiming the lives of Rand's mother, Tiga, and Ray. Also, one of the evil church's priests in the town of Gate claims to have suddenly realized what a dreadful mistake he made regarding the sealed evil and that only the thief Patty can fix it, forcing you to go find her and bring her to Gate. At that point, he betrays you, reveals he's actually the evil church's pope in disguise, and tries to sacrifice Patty to open the gate to Hell. Patty chooses this moment to reveal that she's your long-lost sister Yua. Fortunately, Ryu and Yua's mother steps in to save her.
Also, at the end of the credits after beating the game, at least for the GBA remake, you see art of someone with dragon-like wings standing on the branch of a tree, watching the Township. This is most likely Yua.
Not to mention that when you attack the evil machine that channels prayers into the villain's demonic god, you encounter a man trapped in it, begging to be killed along with the machine. While you can avoid killing him with great difficulty, most players don't know this and simply kill him, causing him to reveal that he is of course your long lost father in his dying breath.
With the bonus that killing him renders it impossible to get the good ending.
Made worse by the fact that the final confrontation with Balio and Sunder has them combining into their "true form", Stallion. The resulting boss fight, consequently, is against a Shout-Out of Ultraman rather than the sneering, brutal enforcers you've grown to hate, and is much less satisfying as a result.
Whilst we're talking about this trope in IV, there's Fou-lu's entire storyline with Mami...right as it looks like they're getting attached to each other (and after no less than two attempts to kill the God Emperor by his empire, the latter of which is rather displeased at the reawakening of their King in the Mountain) Fou-lu is forced to go on the run and Mami is captured (who ALSO ends up dead thanks to Yuna—this time being used as a human warhead for the Carronade). Her literal last words to Fou-lu are that she was hoping they could live together in a normal life—that she knew it was impossible but she still hoped for it. The latter Player Punch is what sends Fou-lu into full-blown Kill All HumansWoobie, Destroyer of Worlds mode (as opposed to being a mere Woobie).
And have we mentioned the manga version manages to be a Reader Punch in both of these segments in an even deeper manner than the original game?
The general conclusion to be drawn is that, while Ryu (the hero) in each Breath of Fire game is supposed to be a different character, it seems that keeping his siblings alive is not one of the typical incarnation's strong points.
Breath of Fire: Dragon Quarter has quite the slap in the face at the end of the game. Throughout the entirety of the game, you have a meter which slowly fills with each transformation into Ryu's dragon form as you try to guide Nina to ground level. If the meter ever fills to 100%, Ryu dies and you have to restart the game from the beginning. Near the end of the game, you're forced to bring the bar to 100% in the very last battle, which subsequently has Ryu dying mere steps from the surface.
Ryu gets better. The very end of the cutscene before the credits has him talking to Odjn, and Odjn bringing him back to life. But just barely.
In Geneforge 2, your teacher Shanti is captured when she goes scouting ahead of you. Much of the middle section of the game revolves around finding her. When you finally do find her, she's been murdered, dressed in a slave's robe, and dumped in the woods. Definitely an It's Personal moment, and it makes your revenge against Stannis much more satisfying.
Not a death example, but definitely a Player Punch: In The World Ends with You, Shiki is taken as your Entry Fee for Week 2, and you spend the next two weeks trying to get her back. She comes back right as you're about to fight yet another part of the final Boss Rush... and then she gets possessed by the Big Bad.
Beat's Start of Darkness was also Player Punch material even earlier than that - as early as Day 4 of Shiki's week. For you hectopascals out there, that's when Rhyme gave herself to save Beat from a Noise ambush.
And then the game goes and socks you again during the third week. Watching helplessly as Konishi grabs Rhyme as Beat's entry fee and painfully crushes her back into pin form with that horrible little smirk on her face is absolutely brutal.
Especially given the sound effects used in that scene. It's so sickening, it's still hard to watch, even after four or five playthroughs.
Hell, the scene where it's revealed that Shiki is the entry fee for the second week itself is a Player Punch, considering the fact that she won The Game and was supposed to go back to life, complete with "ascending into the heavens" imagery. By the same token, the scene in the third week, when Neku realizes that the entry fee that was taken was all the other Players, making it impossible for him to play the game, much less win, prompted a whole "you bastard" sentiment towards the Big Bad.
Not to mention the fact that before you fight Minamimoto, Neku finally finds out how he died - not being shot by Joshua, but being shot by Minamimoto. Seeing the happy look on his face whilst looking at the mural, and then events that follow....ouch. And because Minamimoto is That One Boss, you get to see Neku's death over, and over, and over...
Then at the end of the game, you find out it really was Joshua who shot you. This made a lot of people hate that white haired sissy.
Talking about Joshua, just when he finally stops seeming like a jerk, Joshua gets killed trying to save you.
As mentioned in Kick the Dog, in The Bard's Tale - modern version, the player can be nice to a little dog who then follow the Bard and be cute. A Druid will eventually send a big flying beast to snap the dog's back, killing it. This player purposely chose the 'bad end' to spite the Druids because of this. Even though you can get a ghost of the dog later on, they still killed your dog!
Playing through Legend of Mana on New Game+ to be absolutely heartbreaking (but otherwise doesn't suffer from this on any other game with that feature). Something about interacting with this world when nobody other than me remembers how everything is going to turn out just about slayed me. (Then again, it didn't help that all of the major story arcs either a Downer Ending or Bittersweet Ending.)
The Jumi arc? An exemplary example of Player Punch in a lot of places, granted, but everybody came back, including the player character, the Jumi capital becomes an inhabited city again, and you can still take Elazul, Pearl, and Black Pearl along on your quest after the end of the arc. Doesn't sound much like a Downer Ending.
In Seiken Densetsu 3, one of the main characters, Kevin, is a beastman (basically a werewolf) who is a misfit/outcast because he can't transform into his beast form. As such, he spends most of his time in the forest with a wolf he raised from a pup, Karl, his only friend. Within about the first minute of starting his scenario, Karl transforms into a much larger wolf and attacks Kevin, forcing him to kill his only friend. The reason for Karl's transformation? Deathjester.
It turns about to have been a very convincing illusion meant to bring out his transformation though great anger. It was so convincing that the one behind it had to hurry to dig out the still living Karl from the grave Kevin buried him in.
And then there's Hawk and Lise's story. Isabella/Bigieu usurps the throne of Hawk's kingdom, murders Hawk's best friend, frames Hawk for the murder, threatens to kill Hawk's lover (and the sister of the murdered best friend) should Hawk tell the truth, and then proceeds to invade other kingdoms (including Rolante, resulting in the death of Lise's father and the abduction of her brother) and revive the God-Beasts, with the intention to rule the world (sort of).
In the original Final Fantasy Adventure, the hero has only one longtime friend - Amanda, who was in the same slave pits as the main character. Both escape separately, and he later meets up with her when she's looking to get the tears of a medusa to cure her brother's Baleful Polymorph. You confront the medusa together, defeat it... and cannot find any tears. And then, Amanda finds that she's been poisoned by the medusa and will become one herself. She then cries, making the cure for her brother, and begs the main character to kill her before she starts terrorizing innocents. Killing her is one of the hardest things to do emotionally.
Later, when climbing the tower to reach the Mana Tree, Robot Buddy Marcie does its best to be helpful, and shows itself to be remarkably empathic. When the Load-Bearing Boss goes, Marcie offers to throw the hero across and then jump before the tower crumbles - but reveals after throwing him that it can't, and lied because the hero would have wasted too much time trying to save it when it was impossible. Watching Marcie go down was heartbreaking - at that point, beating the game is arguably more about fighting on in the name of all those who died for you rather than saving the world.
Not that it helps that after all you have been through, the only way to save the world is to have your heroine sacrifice herself to become the Mana Tree.
Speaking of the Mana Tree, there's the Player Punch in Secret of Mana. Namely, when you find out that the main character's mother was the Mana Tree, and that his father was the ghost he saw after removing the sword. Oh, and lest we forget... Flammie's parents. Minor compared to the first one, but still caught you off guard.
And then there's the part when Thanatos forces Dyluck to kill the Girl (she got better).
To be fair, there is a "right" choice: choose Arcia. Laramee is a mere human, and will actually be consumed by the McGuffin, but the game has been throwing not-too-subtle hints at you that Arcia is not entirely human, and in fact her ending shows that she was a servant of God, and God called her back to his side after you chose her.
Late in the game if you take Robo home to future, you can find his girlfriend Atropos XR and find out that she's been reprogrammed and tries to kill Robo forcing you into one of the most painful one-on-one boss fights in video game history.
Chrono Cross. For people who had played it's predecessor, Chrono Trigger, these three words during a confrontation with FATE brought tears to more than a few eyes: "Now eliminating Prometheus."
To elaborate, Prometheus is better known as Robo, your Robot Buddy party member from Chrono Trigger. Now, up until that one scene in Chronopolis, Robo had not appeared in Chrono Cross at all. He was not mentioned at all. None of your party members have any way of knowing who he is. He appears out of nowhere, delivers two or three lines of dialogue, and is killed, while Chrono Cross's cast is probably wondering who this robotic voice is and why they should care. His death basically serves solely to piss off any Chrono Trigger fans who picked up the sequel, which is part of why some of those who liked the former haveissues with the latter.
On a related note, the new endings for Chrono Trigger DS that help tie the game in with Chrono Cross have inspired similar outrage, confirming that yes, Guardia will fall to Porre, and Dalton of all people has a hand in it. Not to mention strongly implying that Guile, a bland, masked magician in Chrono Cross who was originally intended to be Magus in disguise, was really an amnesiac Magus all along, robbing his story of any resolution.
Arguably occurs in Mega Man Star Force. Partway through the third game, in a series that only has the villains bite it - and even then, not too often - you get to watch as the main character's best friend is quite literally blown to pieces. The effect would have been improved if not for the fact it turns out to be a Disney Death.
Fallout 3 has one(In an already Crapsack World) with Harold the lovable ghoul from the first two games has been taken over by Bob and you have to kill him to set him free. To prove you are a heartless shell of a man you can SET HIM ON FIRE!
...or you can Take a Third Option and actually use the tree-Harold combination to start purifying the Capital Wastes, and when you talk to Harold he'll actually be pretty happy that now he's useful and helping others.
The player must also watch his own father flood the control center of Project Purity with lethal radiation in the hopes of keeping it out of Enclave control. After watching this man spend his entire life trying to bring safe water to the people, he sacrifices himself to stop a fascist paramilitary organization from confiscating it, while his only child watches. To top it off, his last action is to look the player character in the eye and gasp, "Run. Run!"
Despite (or perhaps because of) being just a dog, many, many players hit quickload whenever Dogmeat is killed.
Hence why Broken Steel introduced the Puppies perk. And then of course there is the very popular bug that makes Dogmeat nigh on invulnerable. And the players rejoiced.
Many, many players also broke their quickloading keys in the Mariposa Military Base in Fallout, where trying to keep Dogmeat alive was an incredibly arduous procedure, and reloading to revive him was a common occurrence. Even more common than how many times you accidentally blew him to pieces in combat
Should you broker a 'peaceful truce' in the Tenpenny Towers quest, you can come back later to find that the ghouls have slaughtered all the humans and stacked their bodies in the basement. Most Tenpenny residents are unlikable anyway, but knowing that your actions led to the death of Herbert "Daring" Dashwood, the one man who actually respects ghouls and had one as a best friend is a hit.
Roy is entirely to blame for this. Kill him before he enters the tower (so as to not make everyone else hostile) and no harm will come to Tenpenny's human residents.
If you complete Trouble on the Homefront in favor of Butch, and destroy the vault, you get a string of random encounters where you find the corpses of various people from Vault 101, leading up to a brief scene of Amata being executed by Enclave soldiers. While it's possible to prevent her dying by killing the soldiers before they attack her, she will still blame the player.
There's a string of them in Fallout 2. When you reach the object of your quest, the Holy Thirteen (the vault that you start from in Fallout) you are not greeted by the humans you expect, but Deathclaws. Then you realize that the Deathclaw is screaming "Don't shoot" and it's actually friendly. So you make friends with the Deathclaws, do a few quests, and they reward you with the G.E.C.K., the artifact you're questing for. So you cruse back home, expecting a hero's welcome. What you get is a wrecked village and a dead shaman. You learn your people were abducted so you set out to look for them. Eventually, you find yourself in the region of Vault 13 and decde to pop in for a visit. So you go in, and "Where did all the deathclaws go?" Accessing computer records you learn that the Enclave massacred them.
Mother 3 kicks the player in the crotch repeatedly in the first chapter. First, Flint's wife, Hinawa, dies, and he is notified via one of the most painful Can Not Spit It Outs ever. The chapter's boss is the mother of a Drago family that was friends with Flint's children, cybernetically modified into a killing machine. After the battle, the player is shown the broken body of Flint's son Claus lying in a canyon.
And just to take it beyond this, it goes as far as Shooting The Shaggy Dog by making the final battle put Lucas, all by himself, against a completely emotionless version of Claus. You can win without ever making a single attack, but no matter what, Claus kills himself by shooting a deadly lightning attack at you, which the Franklin Badge will reflect.
Lost Odyssey inflicts the player with this trope approximately every ten minutes with their borderline-Narm "dream" short stories. Oh, and Kaim's daughter dying. And a city of people getting wiped out. And Seth sacrificing her happiness and immortality to save the others. Of course, after a while you sort of get used to it.
In Shadow Hearts, Yoshiko Kawashima starts off as an antagonist but later becomes a respectable ally. You leave her in Asia in the first half of the game, only to be sucker punched with the news of her supposed betrayal by her father and death, complete with it playing out on-screen.
Making it worse: her death is one of the primary motivators for the final Big Bad of Covenant.
Also gutwrenching is the true ending to Shadow Hearts. In it, it's assumed that Yuri was unable to defeat the Masks that guarded the Door of Death in his soul's graveyard, and as such Alice if forced to fight alone when the Malice comes for her soul. The game then drags it out and forces you to watch as Alice slowly loses her life force, growing weaker as the party rush to the final boss fight, but refusing to lag behind or get in the way. Then, just when everyone is settling down to a happily-ever-after and Yuri is taking her home to see her mother, she dies in his arms, and despite all Yuri's promises to protect her, there's nothing he can do.
The Elder Scrolls IV: Oblivion: If you play through the Fighter's Guild quests, one involves helping a sweet young lady who owns a settlement near the south of Cyrodiil. Later on, you infiltrate Blackwood Company and help kill goblins at the same settlement. After this, you pass out and wake up elsewhere. When you travel back, you find that the goblins were the result of a drug-induced haze, and you actually killed the lady you helped earlier on.
In the quest Caught in the Hunt, a poor old man who is addicted to gambling starts borrowing money from a criminal Orc named Kurdan. When he can't pay his debts, Kurdan sends him to a fort with the assignment of finding a rare axe there. But it appears the fort is part of a hunting game on human(oid)s and the only way to escape is via a key found inside the fortress, which is filled with hunters. When you return from the fort, Kurdan kills the old man and proclaims he is free of his debt, while gloating. This is the moment where you just know Kurdan must die.
During the Dark Brotherhood Questline, you have to kill a sweet old lady AND her entire family. That was the only assassination in the entire quest line that made me ill. It doesn't get better with repeat play either. Oh, and if you REALLY want to be an heartless scum, you can tell to one of the lady's sons that his mother "bled likea pig" before killing him. He doesn't take it well. Not AT ALL.
Sadly, that is the single best way to deal with him thanks to the guard that seems to live there. He attacks you in revenge for his mother, and the guard kills him for assault. You get off completely scot free considering the guard doesn't hear the comment.
Also during the Dark Brotherhood questline, you'll eventually be ordered to kill everyone in the Cheydinhal Sanctuary. Everyone who was so helpful and friendly to you. Even M'raaj-Dar, who decides to stop being a jackass and be friendly to you.
Bonus points for twisting the knife: you don't realize M'raaj-Dar has warmed up to you until you've been given the order to kill him.
Another one in the Dark Brotherhood questline: Visit The Grey Mare at anytime after Baenlin's death, and you will find his trusty manservant Gromm sitting in there, crying his eyes out over his employer and father figure.
Or we could just sum up: Stay the hell away from the Dark Brotherhood quests unless you like feeling like a rank bastard.
In the Shivering Isles expansion, Sheogorath runs out of time, and he becomes unusually unhappy. Then, he transforms into Jjyggalag and the player must fight him later on. It is the last time the player ever sees Sheogorath (besides themselves).
About halfway through the Mages Guild questline, just in case there was any lingering doubt that he was a monster, Mannimarco torches the Bruma Mages guildhall, and almost everyone in it. No seriously, it is literally wiped off the map, and nearly every single one of its inhabitants die horribly. The Shrinking Violet alchemist? Dead. The hilariously incompetent Pointy-Haired Boss? Dead. The laid back, fun loving, jovial Altmer jokester? Dead. The lovable Khajiit prankster? He survives, but is deeply traumatized by the experience, and its implied that Manny knew he was there, but let him live just to mess with his head. That is it. The Order of the Black Worm is going down HARD.
For some players, any time their horse is attacked. Especially if the horse is killed.
Killing Paarthurnax. He doesn't fly off until you chip away 50% of his health, and seems to try to plead with you as you attack him initially. Not to mention, he's only level 10, which is much weaker than the majority of dragons. It really does feel more like murder than a fight.
For Imperial-aligned players who still sympathized with the Stormcloaks' views, killing Ulfric can be a slug in the gut. The contrast in the attitudes of Tullius and Rikke can be jarring: the latter finds the whole thing tragic and offers a prayer for him, while the former casually rolls off that they'll just put his head on a pike as an example.
Narfi's side quest. You can either inform him about his sister's death and crush his spirit, or lie to him to give him false hope, which could potentially crush him worse down the line. What's worse, he's one of the contracts for the Dark Brotherhood. The sad part, besides killing him, obviously, is that he's a destitute beggar who lives by himself, so it is possible that the mark was made on him out of pity.
There is a brief scene in KotOR II when G0-T0 senselessly murders Remote, the adorable little training droid that follows Bao-Dur around and helps you out faithfully. Fortunately, it got better. Unfortunately, G0-T0 then is implied to murder it again on Malachor V if you don't activate the mass shadow generator. Also, Dark-side ending when everyone left on the Ebon Hawk falls into an abyss.
The Tomato Surprise was a big one for Light Side players. Double it if you played Light side female with the Carth romance. You're giving credits to beggars, restraining yourself, reuniting families, petting kittens, and being a first-rate example of Lawful Good...Oh Crap. What did that bastard say, Carth?! And here's Malak himself - stand back! I Am Who??!
Taking the Dark Side Path? You might regret doing so when you're forced to slaughter over half your crew. Juhani and Jolee are hard enough, but having to kill Mission, even as the girl is insisting down to her last breath that she's still your friend? Talk about Video Game Cruelty Potential. Even nastier is if you force Zaalbar to do it! More than one player reported breaking their X-box controller by dropping it in shock.
In the second one, on Peragus Mining Station you can watch a holovid showing all the miners suffocating from poisonous gasses, right over the places where their bodies are now lying. Made worse by the knowledge that it was completely unnecessary.
Persona 4 Nanako, the main character's cute lovely cousin got kidnapped after the main character and his uncle tossed the Idiot Ball at each other. She dies shortly after you manage to rescue her from the TV world. If you go for the worst ending, she'll be Killed Off for Real.
Worse yet, because the game is all one epic Mind Screw, if you give into your rage and kill the (supposed) bastard who did it, you GET said worst ending.
It's even worse than that. Before you can even determine your ending, you have to watch her death scene anyway, with her father only making it there after she's flat-lined. Forget Player Punch, that was a Player Hit-and-Run.
The eerie silence of your home for the rest of the game, especially the lack of Nanako's cheerful "Welcome home, Big Bro!", is a Player Punch in and of itself!
In Riviera: The Promised Land, there's the end of Chapter 6. So Ein, who has just spent the entire chapter freaking out over having to fight Ledah, has just done so. And even though Ledah has told Ein to kill him, Ein refuses because Ledah is still his True Companions. Oh, wait, here comes Malice, STABBING LEDAH IN THE BACK. ...But Ledah is still alive, so it'll be fine! ...Not for long, as after you fight Malice, he pulls a Heroic Sacrifice to save Ein from her sneak attack. And then, in his death scene, he barely manages to explain what's going on and why he is the way he is (i.e., he has no emotions anymore) before he dies. The entire thing is an evil cycle of worry, relief, and then trauma. Worse, it's the end of the chapter, so there's no direction for your Unstoppable Rage.
Made far, far worse by the fact that Ledah, being rid of emotion for the entire game, actually shows some... before he dies. Sadness ensues.
In Yggdra Union, two battlefields after you meet Roswell and Rosary, you are forced to kill one of the two. Then, in Battlefield 33, you have to face the one you killed again, just to rub your nose in it. Both of Kylier's deaths also count—her Heroic Sacrifice is the climax of a battlefield that's basically one continuous Tear Jerker, and then there's goddamn Battlefield 46. She Came Back Wrong, she's a People Puppet, but Milanor loves her and can't believe he has to fight her. So Yggdra decides she'd better Shoot the Dog. Thing is, Yggdra is the player character, so you're stuck with doing it. AUGH.
Fighting Nordische and Pisce after their Transformation Trauma incidents in Knights in the Nightmare. Especially Nordische, when you consider that the Wisp contains King Willimgard's soul, meaning that he has to fight his own beloved son.
Alighierie's death is one too. Again, doubly so when you consider the spoiler above.
The Your Princess Is in Another Castle scene is also one. After defeating Melissa (or Marietta), you and your heroine run to confront Big Bad Zolgonark only to realize you have no way to defeat him yet. When Zolgonark tries to attack you, she leaps in front of you to shield you from the blow, giving you a slim chance to escape and find your body. The last you see of her until the end of the game, she's still standing steadfastly to take a blow that whites out the entire screen, her pleas for you to escape trailing off into silence. This is bad enough, but when you finally arrive to fight Zolgonark again, you only see her faint white outline, the same as the souls of the dead. Ow, that was my heart. It's hard enough to watch Maria do this, but seeing arrogant, self-concerned Meria throw pretense to the winds and do the same was just too much.
The series as a whole has two huge ones in the form of Nessiah and Marietta, who are both victims of Hector's schemes.
Dragon Quest V does this to your dad, then to your wife, then your cat, and then tops it off by doing it to YOU! Ow.
It also does a few more if you don't marry Bianca (Which the game really wants you to). Gee, why did you gave us a choice then, game? Fortunately, the remake of said game averts this - while Bianca is still considered the canonical choice, you no longer need to feel like a bastard for not choosing her.
Star Ocean: The Second Story (As well as its remake, Second Evolution) did this with the death of Ronixis at the hands of Gabriel and Lucifer. Ronixis was one of the major protagonists from the first game and was killed in a particularly tragic fashion (Thinking his son was dead and his wife hated him.)
Also the end of both discs of the Playstation version of this game. The first disc ends with the destruction of Planet Expel by the Ten Wise Men. As bad as that is the second disc is even worse considering that the Nedians can actually Set Right What Once Was Wrong in this case, but it comes at a very high price considering that it takes all of Planet's Nede's energy to restore Planet Expel and its entire population, which in turn destroys Planet Nede in an epic level Heroic Sacrifice.
This whole sequence makes you want to recruit Noel and Chisato even more, considering one of the last quotes of the game.
Before that, we had the original Star Ocean as well as First Departure, in which Asmodeus' destruction of a small town is immediately preceded by a scene focusing on a little girl in said village that you had the opportunity to spend time with, building snowmen.
The Suikoden series is full of these to the point where you need a helmet, face mask, mouth guard, and a box of tissues to make it through.
At one point in the game, most of the Dragon Knights' dragons become sick with a rare disease that can only be cured with special ingredients. Dr. Liukan says that one of the ingredients is a special flower that the Big Bad currently has, and doesn't mention the last ingredient. Futch the youngest dragon knight and his dragon named Black go and retrieve the flower, but are attacked after getting it. Futch manages to survive but Black isn't so lucky. The sad thing about this is the reason that Dr. Liukan was hesitant to mention the last ingredient was because it's a dragon's liver, which meant that one dragon would have to die to save the other dragons regardless of the circumstances, and that they took Black's liver from his corpse to make the cure to save the other dragons. A huge Player SuckerMegaton Punch comes after this sequence when Futch recovers and learns what happened and also that by the Dragon Knight code, any knight who loses their dragon for any reason is expelled from the Dragon Knights, which leaves Futch homeless until Humphrey takes him on as his pupil, and they join your army.
Also in the end learning that Sanchez's betrayal and assault on Mathiu ended up killing him, considering the fact that Mathiu dies shortly after hearing about your army's victory.
Liukan: "Rest in peace, Master Mathiu."
The Witcher attempted this with White Rayna, giving her the most dramatically extended death in the game, during a cutscene. This worked to varying degrees. Fans of the novels knew her better as the genocidal Black Rayna, and even fans not familiar with that background found her to be a throwaway Replacement Scrappy while the hero's chosen love interest was out of the plot. Reviving her as a mind-controlled zombie mutant may have been a more successful attempt at doubling the punch; at least players who took advantage of her Optional Sexual Encounter could be uneasy with having to kill her themselves.
The fact that she was one of the most repulsive characters in the game didn't help her case either.
Finding the Dimeritium Medallion on the body of the Big Bad at the end was probably a more effective one.
Marvel Ultimate Alliance makes you choose between saving the life of Nightcrawler or Jean Grey. The ending you get from saving Nightcrawler is preferable (if he lives Jean comes back as Dark Phoenix. If he dies Professor X is assassinated by Mystique), but you can bet some fans were torn by the choice, especially since Jean is something of a Chew Toy, and it'd be nice to give her a break for once.
Ultimately subverted for those who decided to save Nightcrawler, as MUA 2 shows that Jean's case was resolved cleanly by virtue of her being a secret playable character.
Shin Megami Tensei III: Nocturne has quite a lot of these actually. Given the post apocalyptic tone of the game, it might not be unexpected, but it is still surprisingly effective : The Mantra, although a quite brutal bunch appear at first to be some sort of Proud Warrior Race, who respect you as soon as you defeat their champions. Given the state of the rest of the world, they can be somewhat sympathetic. Then, Hikawa casually unleashes the nightmare system that wipes out most of them before including their leader who breaks down (literally) in front of you. Then, you get to the Kabukicho Prison the not that nice after all Mantra used to torture Manikins, the weak race of the game. These Manikins later gather into a small town, only to be slaughtered by the resurrected Mantra, which lets you witness just how horrible their values really were. Oh and your two human friends end up turning against you too (except if you endorse their reason, but at least one has to die).
Persona 3 has first the death of Shinjiro, then Chidori's Heroic Sacrifice to make the player hate Takaya's guts. Though Shinji was going to die anyway, and was almost killed by Ken, which can prove frustrating to the players who then have to have Ken in their party for the rest of the game.
Persona 3 pulls off one of the ultimate Player Punches in the last scene of the True Ending, where the Protagonist must sacrifice himself in order to save humanity. And then, he holds on anyway, carrying the essence of death within himself, just to fulfill his promise to his friends to meet them on the last day of school. Then, in an incredibly heartbreaking finale, he dies.
Even worse, he dies right when everyone arrives.
FES adds a scene where Chidori is revealed to have survived, probably so the player doesn't get bored with Heroic Sacrifices before the end. And, apparently, playing as the female protagonist in Persona 3 Portable allows you to indirectly save Shinjiro's life in which by doing so, he fell for her. Which just makes the last punch hurt that much more, since she won't get to spend her life with the man who's only alive because of her love.
In the girl's route of Portable, even if the game is slightly different, you know what's gonna happen. Considering how cheerful the female protagonist is, and learning more about your party members through the social links, you can sense the punch, but it won't help the sting. A striking one is that if conditions were different Shinjiro and Ken could have been good friends, as they make mentions of each other in their social links, and the player would notice their similarities in ideals.
Then there's Akinari, the Sun Arcana S.Link. Sure, he tells you upfront that "Any day now, I'm going to die", but still. The worst part is he dies having only just found a reason to be happy to be alive.
There's more than one painful death in Last Scenario, but one near the end that really does it is Alison's Heroic Sacrifice to save the party from Tiamat. It's made especially frustrating by the fact that Tiamat blows both of them up, so you don't even get the satisfaction of destroying her in another boss fight.
The prologue of Valkyrie Profile: Covenant of the Plume ends with a fight where you're forced to use the Plume on your best friend Ancel, who is built up as a main character and has a love interest. For reference, using the Plume turns a party member of your choosing into a walking Game Breaker capable of single-handedly winning the current battle, plus it gives you a technique that is a Game Breaker in of itself. Sounds cool, right? Well, there's also a small problem you aren't aware of at that point, namely that it sacrifices their soul.
Live A Live is practically made of Mood Whiplash, and pulls this off very successfully a few times over. About half of all the characters end up dead, but because it's an entirely different story each time, you'll care just as damn hard for each and every one of them. Then, just as you're sort of used to it, and you're identifying with all of the main characters so hard because of the long series of Player Punch moments in the first half of the game - you enter the second half, entirely unexpectedly, and you'll find out who was behind all of the deaths. And you'll cry. Because he turns out to be a Noble Hero who just kind of had a really bad day. And became Woobie, Destroyer of Worlds as a result. And you get to play every moment of it.
In Etrian Odyssey: Heroes of Lagaard, the player gets punched when they find a wounded Kurogane and realize what happened to his partner Flausgul... It's particularly jarring because they appeared to be getting set up as recurring characters you could expect to meet in the labyrinth far more often than you actually do to get see them.
And in The Drowned City, something similar occurs with the Murotsumi Guild — only this time, the player has to choose whether it's Agata or Hypatia that dies.
Dragon Age: Origins delivers one early on with the deaths of Daveth and Jory, your fellow Grey Warden recruits, during the Joining. Even the PC looks stunned when Duncan kills Jory. But the shocks don't stop there, as the game turns this trope Upto Eleven with the death of Duncan.
There's at least one extra one for every origin, as well, some during, some when the PC comes back into contact with their old life. Dalish Elf origin... that'll leave a bruise.
In addition, realizing that Lothering is destroyed, especially if you took the time to talk to everyone, especially the elf family and the little boy whose parents are (apparently) dead. Also Redcliffe, if you decide to (or accidentally) leave in the middle of the first big battle there. And the werewolves origins... and the entire game. Really.
If you play as a female Warden romancing Alistair, everything from the Landsmeet to the endgame can be one long sequence of player punches. If you make Alistair king, he will dump you directly after the Landsmeet unless 1) you are the human noble and already proposed to him during the Landsmeet, or 2) you "hardened" him after he met Goldanna - in which case you can be his mistress, even though he'll have to marry someone else. (If you're playing a good-aligned everyone-deserves-a-second-chance type, you may get another nasty shock as Alistair dumps you and the cause you've been fighting for in favor of revenge.) Then, after you find out the truth about why only Grey Wardens can truly defeat the archdemon, you'll have to persuade him to father a baby in a blood-magic-fueled sex rite with Morrigan, whom he hates, if you want both of you to survive. If you refuse to follow Morrigan's plan, one of you will die. Even if you intend to make the sacrifice yourself, Alistair will take the decision from your hands and sacrifice himself to save you unless you leave him at the gate.
The human noble origin is chock full of these. You're introduced to plenty of decent, likable characters, including your doting Reasonable Authority Figure dad, your loving unexpected Action Girl mom, the loyal and brave knight Ser Gilmore, your kind and pious sister-in-law Oriana, and (worst of all) your adorably enthusiastic and naive nephew Oren. And they all die. And you can't stop it. Even worse, if you choose to get to know Dairren or Iona a lot better, when the soldiers storm your room they'll be shot dead right in front of you before you can do anything. Howe is going to pay.
Completing Orzammar can have this effect if you decide to make Bhelen king. His first royal act is to call for the execution of Harrowmont, his father's closest friend and advisor... who just accepts it without a fuss. It's even worse if you've played through the dwarf noble origin and seen firsthand what a kind, fair, reasonable character Harrowmont truly is. The really sad part is that even if you make Harrowmont king, he still doesn't have a very good fate.
The Awakening expansion DLC has a very mean one in the form of Mhairi: She helps you all the way while freeing Vigil's Keep, stating all the time how eager she is to become a Grey Warden. You can even (unlike other temporary companions) gain approval with her. Heck, she even had an own gameplay trailer. Then she dies during her Joining.
And later on, leading up to the final confrontation, you're forced to choose between defending Amaranthine City (where you've done quite a bit of adventuring and trading and which you have been repeatedly told is a culturally and economically important city) and defending Vigil's Keep (where all your friends not currently in the party are hanging out). If you decide to defend Vigil's Keep, you have to watch while your soldiers burn Amaranthine to the ground. This is made worse in retrospect by Guide Dang It: if you make exactly the right choices before that one, the consequences of this particular choice are made a lot less dire, but it's far from clear at the time what the "right" choices are supposed to be.
Dragon Age II has the "All That Remains" quest, in which your mother is kidnapped and mutilated by a blood mage trying to reconstruct his dead wife.
At the end of the prologue, one of your siblings has their head bashed in by an Ogre. At the end of chapter one, you lose whichever one remains (to death, to the Grey Wardens, or to the Templars/Circle, depending on your choices). That actually makes "All That Remains" all the more powerful, as Hawke loses his/her entire family.
Near the ending of the game, Anders blowing up the chantry can feel like a Player Punch, especially if you've befriended him and especially if you've romanced him. It's even worse if you helped him with his final companion quest, where it turns out he manipulated you into gathering the last components for his bomb and unknowingly helped him get it into the chantry. To make it worse, the game then puts it into your hands whether he lives or dies. You can either kill him, which is a pretty heartbreaking scene, regardless of how you feel about his character, tell him to leave, or keep him around knowing that the trust between you has been shattered forever. And if you romanced him? The only way you can get something resembling a happy ending is if you side with the mages at the end and agree to go on the run with him as fugitives with pretty much every Templar in Thedas out for your blood. OUCH.
Quite honestly, the fact is that no matter how hard you try to prevent it, the city falls into chaos and everybody (except you and your friends) ultimately goes crazy and gets killed, leading to a massive Downer Ending. This is arguably the worst Player Punch in the series to date.
Combined with Tear Jerkers and Heroic Sacrifices, Infinite Space has lots of this, although a few of them can be avoided depending on the routes you take. The most notable one is Lord Roth and Nele's death, which happens if you didn't recruit Katida, turning her into an Ax-Crazy in Act 2.
Avalon Code drops one of these on you midgame; your best friend betrays you, and hands the Book of Prophecy off to the main villain, whose actions with it scatter your spirit buddies, majorly trash the town, AND cause the book to suck either your Ill Girl childhood friend Fana, or your love interest in whole. And if that wasn't enough, the townspeople, after pulling you out of a pile of rubble when it's over, BLAME YOU EXCLUSIVELY for what happened, instantly convincing themselves that your were the enemy all along. Subverted in that you can save your friend/lover later.
Dragon Quest IX has Catarrhina, who dies literally moments before you manage to seal away the evil spirit causing her town to be infected with a death disease.
Vagrant Story features a cultist named Hardin who is, for all appearances, Sydney's right-hand man. There is also a boy Sydney and Hardin kidnapped, Joshua. Throughout the game, Hardin receives a good deal of character development - we find out that he once had a younger brother, who was very ill. Hardin went to prison for selling weapons on the side (after betraying his fellows in the hopes that doing so would allow him to go free), and while he was in prison, his brother died. It is heavily implied that Joshua reminds Hardin of his brother. And then, at the end, we get to watch Hardin die slowly, while Joshua speaks for the first time - "No, Hardin! Don't go!" Ouch.
Planescape: Torment has you, rather often, encounter traces of your previous Incarnations. One of them is the walking Moral Event Horizon moment knows as the Practical Incarnation. And should you join the society of sensates, you can experience the memories and emotions of a woman you first encountered as a spirit at the Mortuary. The private sensorium that contains that stone has two others - one is actually a trap from a past incarnation and a Room Full of Crazy, the other is the experience of being masterfully tortured by an ancient hag. And they're still better than that one.
There's also the Fortress of Regrets, in which the party members you've cultivated throughout the game are exterminated one by one, and all you can do is watch.
Made even worse because each of them is given the option to go home, and they all stay to face certain death for you.
Alpha Protocol's final mission in Rome. Madison has been kidnapped, and Marburg is setting up The Sadistic Choice between saving her or disarming the bombs that will kill hundreds of innocents. Choose to save Madison, and the bombs will blow and she'll berate you for putting her life over hundreds of others. But disarm the bombs, and Marburg will kill Madison right in front of you, for no reason except because.
Valkyria Chronicles has Isara, Welkin's cute, sweet adopted sister, gunned down by an Imperial sniper halfway through the game.
Not to be outdone, the sequel has the Rebels attacking the military academy halfway through the game, slaughtering hundreds, if not thousands, of hapless students, ultimately culminating in Juliana being brutally murdered by The Brute, just as she finally becomes likable. Oh, and then the school's headmaster is Driven to Suicide.
Ar tonelico gives you a repeated AND delayed Player Punch. The game starts with Mir, who takes control of the tower where Lyner lives and wrecks total havoc. So, the game starts with Lyner searching for a hymn crystal that will put a stop to Mir, all well right? Totally WRONG. things don't turn out as they should and so comes the first hit. Shurelia dies. After this is solved, you can get an option to either let things stay as they are... or decide to solve the whole Shurelia deal. That is pretty much summarizing the whole thing... but in the game, and if you play both routes, you see that she is more problems than what the eyes can see. She is the reason of why Misha can't stop singing, the reason for the church where Aurica lives to be corrupt, the reason of why Ayatane (Mir's son) fights against Lyner (his best friend) for a great part of the plot, the reason for the world to be in the state that is now, the reason for the Reyvateils to be so overworked and underpaid, the reason for Misha to look like an 8 year old... HECK!!! pretty much every problem in the game... soooooo the bitch's gotta go down right? NO!!! doing so would give you a bad ending... you then set to see her reasons... and learn that she was actually a good girl, but was so pushed out of her limits and abused that she went out berserk and killed almost a third of the world. The punch then comes when you find out (though if you completed Shurelia's cosmosphere level 5 you would still know) that she actually IS a girl (one that looks like a 14 year old at that...) so, who's the bastard now?
Then in Metafalica, you meet Jaqcli come on, if you don't get that she is Mir then you got a problem... HER MIND GUARDIAN IS FRIGGI'N AYATANE!!!! and the punch comes back. In her Cosmosphere not only do you see what she had to go through, but also the fact that even nowadays she repents for what she did... even then you get hit when, if picked a route in level 6 turns out that in level 8 she's dead... no matter what you picked. So you go back and set things right and alls fine... until you meet the "No boundaries Mir" pretty much a full deredere, diabetes inducing, sheer Moe, SWEET girl.. Hell, she even openly says to Croix that she loves him in more than one occasion. The punch? you learn how was Mir before she broke out of her limits... a caring sweet child that not only loves every damn living thing and dislikes war, but also loves her human creators even after all that they did to her, even composing EXEC_HARMONIUS (they rejected that song and that was the first time she knew what hate was... it wasn't pretty...). Now... who was the one that you wanted to kill so desperately in the first game again?
Also, in the first game... Hama "Diying" in Misha's cosmosphere... just after she called Lyner "Daddy" (Note, not "Father", not "Dad", "Daddy", as in "sweet lovely daughter 'Daddy'" if you did not feel anything when that happened, then you, my friend, have no soul.
Baten Kaitos Origins does this extremely effectively when the already Jerkass Shanath kicks it Up to Eleven by ripping out Gena's (the player character's mother) Wings of the Heart as part of a political rally, an action which not only can be fatal, but leaves a survivor bedridden, concussed, and emotionally numb. Sagi himself engages in a Precision F-Strike ("Go to hell, you son of a bitch!") and suffice it to say, the player really wants Shanath to die. Later, when the player is actually given the opportunity to kill him in cold blood, you feel like a total jerk for taking it, because his five year old daughter walks in just in time to be scarred for life. And you know from the first game that that little girl is now an orphan who is raised by the military and grows up to be an emotionally numb, antisocial killing machine that eventually aids a genocide. All because of you. The real kicker? Even if you don't kill Shanath, he dies in front of his kid anyway.
Although the Pokémon series is pretty light on plot and characterization, and so tends to avert this, the "Nuzlocke Run" (based on a series of webcomics with the same name) is specifically designed to set up Player Punches. It limits the number of Pokemon you're allowed to catch, and turns ordinary NonLethal KOs into Permadeaths. The result is that every 'mon you catch becomes a valuable member of your team, and losing one that's stuck with you for a very long time is downright heartbreaking.
N's back story counts for this, but even more so if you played Pokémon Black 2 and White 2 and learn the whole story about how Ghetsis found N in the woods using his special ability to communicate with Pokemon, and adopts N as his own son, pretending to give N the human family he never had, when really all he wanted to do is use the poor boy in order to use him as part of his plan to make everyone else release their Pokemon so that Ghetsis alone could use his Pokemon to conquer the world. This gets even worse if you know this and re-watch the opening to Pokémon Black and White again.
If you think that Ghetsis is a Jerkass in Pokémon Black and White, he takes it Up to Eleven in the sequel when after you defeat Drayden and get the DNA splicers, Team Plasma attacks you and uses a captured Kyurem to freeze most of Opelucid City trapping everyone inside their houses until you storm Team Plasma's frigate,free the Kyurem, and defeat Ghetsis. Yes, Ghetsis must be taken down at all cost.
Also Lake Valor's Magikarp population. Keep in mind that the majority of them probably only have Splash, which does absolutely nothing, leaving them practically defenseless. The Magikarp's home gets destroyed by Team Galactic so that the Lake Trio can be captured, and the Magikarp are left to suffocate. What makes this worse is that it's obvious no one even cares about them. (In most cases probably not even the player.) And even if you did care, you can't help them. You can help the Lake Trio, who are considered cute, and who have a way to defend themselves, but you can't save the Magikarp, who aren't and don't.
And then we get to the Pokémon Mystery Dungeon series. The endings to both games involves your character returning to the human world (Red/Blue Rescue Team) or disappearing forever (Time/Darkness). Both of them are pretty sad, but they're made even more heart-wrenching when the game forces you to watch your partner mourn over you when you leave them. And let's not even get to Grovyle's Heroic Sacrifice...
Golden Sun: The Lost Age is pretty harsh when you realize that the villains of the first game were not Card Carrying Villains as you suspected, but rather Anti Villains who wanted to save their civilization from destruction. Unlike most examples, this is not an in-your-face scene, but a gradual realization on the part of the player over the course of The Lost Age, which is finally fully explored when the characters encounter the hometown of the first game's baddies as the game's end.
The Lost Age punches you even harder when, during the Final Dungeon (Mars Lighthouse) you have to face and defeat two Fire Dragons in a Boss Battle... who turn out to be Agatio and Karst, your Aloof Allies and part-time adversaries who were simply trying to complete Saturos and Menardi's quest (oh, and trying to murder first game's protagonist Isaac, but Karst didhave understandable motives...) It gets worse when they beg you to finish their quest for them, putting their animosity to rest at last. It's Doubly worse with the rather blatant Ship Tease between Karst and TLA protagonist Felix (which has fanfic writers to this very day saving her life). Then, it's Triply worse when you flash-forward 30 years and discover that the Hero Worshipping part of the masses did make the four out as Card Carrying Villains in the textbooks, and because they are already controversial public figures for their actions during the older games, the veteran heroes can't do or say anything to give their dissenters ammunition against them in an already-divided world...
The Lost Age's worst punch was The Wise One transforming the heroes' parents into the Final Boss and forcing the heroes to murder the parents they were trying to rescue as a Secret Test of Character. You have no soul if you didn't react when soft-spoken mama's boy Isaac dropped this line:
"I knew what I was doing the moment I raised my sword."
It can be made even worse when you realise at the end of the game that everything the heroes have done in all three games was orchestrated by the series villain, and that all of this doesn't mean a thing to him.
Golden Sun: Dark Dawn has a pretty heavy one, not only for one game but for the series in general. For the most part, the series is relatively lighthearted when it comes to death, limited only to the villains, extremely minor characters, or offscreen ones for those with slightly bigger roles. Dark Dawn sets itself up much the same way... until the Grave Eclipse is activated. Following this, it's easily possible to find corpses of innocents who had nothing to do with this lying around. Not to mention you can read their thoughts. One particularly poignant example is the Crystallux summon sidequest, which entails failing to save a little girl and burying her next to her deceased grandfather. Also done with Briggs, a returning character from the previous game, who gives a Heroic Sacrifice to ensure the party (including his only son, Eoleo) a chance to escape the ravaged city of Belinsk.
Deus Ex: Human Revolution has several: Belltower's goons slaughtering innocents at Alice Garden Pods just to get to van Bruggen; their ambush in Hengsha if it leads to Faridah's death, especially if you leave the area before the VTOL explodes, which forces you to watch as they execute her in cold blood and start gloating about it and finding Faridah's corpse in the Harvesters' hideout, presumably stripped of augumentations. These three moments were rage inducing enough to make several players give up their Pacifist Runs on the spot.
A non-fatal variant occurs in Inazuma Eleven 2 when Kazemaru, who has been with you through thick and thin since the very first chapter of the first game, is specifically singled out by The Genesis to be the victim of a No-Holds-Barred Beatdown and gets Put On An Ambulance as a result.
Similar to the Final Fantasy VII example above, Mega Man X: Command Mission has one at the end of Chapter 6, when Spider sacrifices himself to get rid of Incentas and open the way for the rest of the party to escape the mines before it self-destructs. The similarity comes in the fact that, like with Aerith, you can still buy Spider's weapons even in the final stage, with the only difference being that his icon won't appear beside them. The game also won't let you sell his starting weapon. Averted, however, when it is revealed that Spider was likely not Spider at all throughout the game.
Summon Night: Swordcraft Story is, for the most part, a sweet, light-hearted Action RPG. You discover that one of the town's leaders is working for the Big Bad, and confront him. It turns out that he's been deluded into it by thinking that he'll be able to cure his Ill Girl sister if he helps. Naturally, the good guys want to capture him and bring him home, as he's clearly not remotely evil, however misguided...but he refuses, in the middle of a wild-eyed Villainous Breakdown, and jumps off a cliff rather than admit defeat. It's deeply shocking in an otherwise-cheerful game.
Xenoblade spends the first few hours of the game developing the main characters and their lifestyles, including the relationship between Shulk and Fiora. Fiora becomes a party member early on, and she is the first character you can improve your relationship with, and come to like her as time goes on. So it becomes a devastating Player Punch when Metal Face, despite her best efforts to protect Shulk and their hometown, kills her. It's made worse in that Shulk sees it happen via a vision before it happens, which serves to extend the tension we feel, while also giving us hope he can change the events of that vision, since he had done it moments earlier.
The eventual fate of most of Alcamoth's population can come as a huge one if you bothered doing all of the quests there. The girl whose friendship you mended? The concerned mother who asked you do the aforementioned deed for her daughter's sake? The father whose lost children you helped locate? They all end up transformed into monstrous Telethia. Worse, their friends and family later ask you to go into the city and give them a Mercy Kill.
Radiant Historia approaches Suikoden levels of this trope, starting about fifteen minutes into the game, when Raynie and Marco die in a Hopeless Boss Fight. Then comes Chapter 2 of the Alternate History, when Rosch's entire brigade gets wiped out, the adorable Mauve Shirt Kiel dies distracting the enemy so Stocke can escape, and none of it can be changed, frustrating both Stocke and the player to no end. The game also forces you into a Fighting Your Friend situation several times, and half the bad ends involve party members and other likeable characters dying left and right. Not to mention the normal ending, where Stocke pulls a Heroic Sacrifice to hold off the end of the world for a few more years. Most of these can be changed or avoided, but it doesn't make them any less tear-jerking.
As befitting the tone of the work, practically no-one in Dark Souls lasts long enough to accomplish much, succumbing to their Dark Sign and going Hollow. The punch comes in that the last words for many characters are them going out from Firelink Shrine to achieve some goal, only to show up unceremoniously as a unique enemy somewhere else, far from their goal.
Also, the death of Solaire. The Knight in Shining Armor, so steadfastly out of place in this bleak world, grows steadily disheartened in his quest for his own sun. Then he comes along a Sunlight Maggot, and promptly goes insane, waiting in a dark and meaningless cave to attack you and be put down. Yes, this can be prevented, but only via an extreme Guide Dang It moment.
Special points go to the aftermath of the Chaos Witch Queelag's boss fight. At first, she just seems to be a random Mix And Match Creature (beautiful female human whose lower half is a Giant Spider) guarding the bell you need to ring in order to proceed. It's only after you kill her that you find her lair beneath the bell tower, and encounter her sister, The Fair Lady. Like Queelag, she's also half spider, but her body is partially crushed beneath her massive clutch of bloody spider eggs. Turns out, she's Queelag's sister, left horribly ill from swallowing her servants' Blight Pus. Y'know, after having barely escaped the ruin of her homeland of Izalith, that was caused by her mother and two of her sisters mutating into an Eldritch Abomination, an event that also made her and Queelag into the Spider demons they are today. Did we mention that of her remaining four siblings one has died died, one has gone insane, one has requested she be Mercy Killed, and one has become anotherEldritch Abomination? Or that the Pus has made sure that none of her children survive long outside their eggs? Or that her voice actress really does sound like a terminally-ill patient who's barely clinging to life? Or that, when you're wearing the Old Witch's Ring, she mistakes you for Queelag (who, remember, you just killed) because you're the only other person who can even understand her language? OUCH.