While the first two Metal Gear games played everything fairly straight, the Metal Gear Solid series is intended as a deconstruction of action movies (and, to a lesser extent, video games), twisting tropes common to them around in extremely horrible ways to establish how damaged everything and everyone would have to be for an action movie scenario to work in the real world. By the second game it's way out into the nastiest parts of the Deconstructor Fleet territory, shamelessly attacking fandom, the video game industry, the expectations of fans and even its own prequel and characters. Some would argue it goes a bit too far, to the point where it feels very painful to play a game which clearly hates you so much.
It should be noted that, except for Metal Gear Solid 2, the series was somewhat affectionate in its dismantling of said tropes. At the end of the day, the heroes find a reason to justify their personal suffering and the battles they just fought.
Finally, Metal Gear Solid 4 raises the question of what exactly happens to action heroes after the action movie ends. The choices that are presented are dying in a blaze of glory, suicide, or falling into obscurity.
MGS4 explores the concept of the Badass Grandpa. Snake's willingness to fight in spite of his advanced physical age isn't solely depicted as being admirable but also as being foolish and suicidal, people who idolized Snake back in the day patronize him and treat him as a burden, and in general Snake's age is the subject of cruel jokes. In fact, Snake's lifebar is changed to Old Snake to emphasize this.
If Metal Gear Solid and later games in the series dealt with action and spy movies, then Policenauts tackled fiction that involved space travel and space colonization such as Gundam. It is shown, said, or suggested in the game that there are issues with overcrowding, assorted denizens are on medications that are of dubious legality, said denizens need to be careful when it comes to their calcium intake, and that humans born and raised on Beyond Coast are taught to act differently from earth born humans to the point there are accents for both of them. And there's even more than all of that, such as how living in a space colony affects sex working. Ultimately, the Big Bad basically says in the Motive Rant that humanity in the universe of Policenauts was not ready to leave Earth, especially seeing as how the Earth's problems still hadn't been properly dealt with, and the player might very well agree with that. As an article on Hardcore Gaming 101puts it:
"Of course, just as Metal Gear Solid was screaming "NUKES ARE BAD" at the top of its lungs, the prevailing theme in Policenauts is "SPACE IS BAD", which is pounded into your head on several occasions."
It is quite plausible to read Half-Life as a deconstruction of the archetypalFirst-Person ShooterDoom. The basic premise is essentially the same; an experiment into teleportation technology goes horribly wrong and creates a dimensional rift through which monstrosities invade our world. Additionally, there is very little plot exposition (just like the original Doom!). But whereas Doom played this incident as a wonderful way to demonstrate one's masculine virility by filling demons full of lead, Half-Life shows you exactly how frightening this kind of situation would be in the real world. You must scramble to stay alive, think and not act like a stereotypical Space Marine in order to remain breathing. Additionally, while Doom had almost no plot exposition whatsoever, Half-Life frustrates the player with its lack of explicit exposition, demonstrating just how terrifying it would be to be stuck in a life-threatening situation with absolutely no information about it.
Word of God is that they weren't trying to deconstruct Objectivism per se, more that they where trying to deconstruct the idea of Utopian fiction (showing that human nature always gets in the way of any so-called "perfect society") as well as the idea of the Übermensch with the antagonists Andrew Ryan and Sofia Lamb (who runs a collectivist society in Bioshock 2).
Portal starts with a fairly common paper-thin puzzle game plot — make it through all nineteen Test Chambers of the Enrichment Center, and There Will Be Cake. However, as the danger level climbs, the explanations you're given for why you're facing such dangers go from slightly unusual to downright insane — then stop altogether. The entire set looks like you're a subject in a deranged Skinner Box experiment. And you start seeing evidence that previous test subjects have suffered nervous breakdowns, been driven to madness, or tried to break out of the test chambers. And then comes The Reveal at the end of Test Chamber 19. You've got an Excuse Plot played for horror. And forlaughs.
Worth noting that it takes place in the same universe as the aforementioned Half-Life.
Star Wars: Knights of the Old Republic II: The Sith Lords has all of the standard RPG conventions; you recruit party members who follow you forevermore, an Obi-Wan equivalent who explains everything, and you gain XP, levels and new abilities through combat. And then several important characters call you out on all of this, saying, "Have you ever stopped to think about how you get stronger by killing everything? Don't you wonder why these people follow you without question? Has it occurred to you that your Obi-Wan only knows so much about both us and the villains because she's worked for both?" It turns out that these standard RPG conventions aren't Gameplay and Story Segregation at all, but rather, things that actually happen in the plot, caused by the plot's Awful Truth. The standard aspects of the genre we as the player take for granted are seen by the people involved not because they can see through the fourth wall, but because any sane person would look at this behavior and realize that it's not the way reality should work, even the reality of Star Wars. Light or darksided, it says something about the Exile that s/he doesn't even notice it.
Not to mention the way it subverts the Karma Meter, by making what seems like the right thing to do end up being exactly the wrong thing to do, as is often the case in real life. For example giving to a beggar could lead to a worse outcome than if you had left him alone, as it makes him a target for armed robbery, and thus getting him killed. This example is the most obvious one in the game, as Kreia will bitch out the Exile regardless of the player's choice, not because she disagrees with the morality involved, but because the Exile (and very likely the player) does not consider the fact that following one's moral code does not exempt decisions from having consequences.
This includes deconstructing the idea of the RPG party and battle system, and at one point a companion tells you it frightens her how she follows you unthinkingly into battle, shoots when you say to shoot, kills when you say to kill etc. As in the above XP Point example, this is framed as a disturbing and unique characteristic of the main character, and treated as a plot point.
It also deconstructs the Jedi and the Sith — Force users in general can often be compared to deities, able to accomplish great feats that a mere mortal would declare impossible. A recurring theme in the game is that there are often times where a Muggle can do things that a Jedi would never be able to do.
Finally, it deconstructs Lucas's presentation of the Force, in that the Big Bad, having sampled from both the Jedi and Sith wells, ultimately rejects both because they're completely opposed yet they both work. Obviously the Force is far greater than they realized and the Big Bad is hoping to destroy the Force itself using the PC, freeing life from its influence.
This article from Cracked proposes an ultra-realistic war game. That is, you spend two hours pushing across a map to destroy a nuke silo only to find out later it was an orphanage, complete with celebrities decrying the attack. Public Support rises and falls depending on entirely arbitrary factors, mission objectives change frequently and without warning, the cool superweapons kill 100 of your soldiers because the contractors cut corners, etc.
Even though Half-Minute Hero's role-playing-game parts mostly ridicule many cliches found in role-playing games, it deconstructs RPG game concept as a whole. Makes you wonder why almost all other role-playing games include hours of Forced Level Grinding and other tedious activities.
The Shin Megami Tensei franchise often plays around with tropes and expectations, but one of the main thrusts of the recent Devil Survivor title is an unrelentingly vicious deconstruction of "Mons" games in the vein of Pokémon. During the course of the game, many people obtain small handheld devices that allow them to summon various kinds of demons which essentially work like the Mons do in other games. Needless to say, it doesn't take very long before many start using them for power, or "justice", or the like, resulting in chaos and death on the streets of a locked-down Tokyo.
Haunting Ground could be considered as a deconstruction of the more typical Survival Horror games where the main character is given all sorts of weapons and ammunition to cut down a near endless stream of monsters. The most Fiona can do herself is kick the enemy, and she relies on her pet dog to keep the enemy at bay as long as she can. The game also has a feature where the main character panics and gets harder to control the more she's hurt, like most real people would do if they were being chased around by psychopaths.
Haunting Ground uses very similar gameplay — and was originally intended as a sequel — to the Clock Tower series, the first part of which was published for SNES in 1995, before survival horror had established itself as the genre it is today. Perhaps a better example of a survival horror deconstruction would be the original Siren, which takes what at first glance seems to be a fairly typical zombie scenario, but instead of handing you lots and lots of guns and a character with a visible health bar, you get a cast of very average people who are clumsy in combat, have a very limited access to weapons (and no access to healing items whatsoever), and die very easily. Instead of fighting everything with wild abandon, you need to be stealthy and avoid close encounters, much like the average joe would have to do in such a situation. The sequels have been gradually slipping into a more conventional, combat-oriented style of gameplay.
The OPENING SEQUENCE of the second game states quite clearly "No Dine, no Knox, no Fair. In other words it is not mystery. But it happens, all it happens, let it happens." The author actually goes out of the way to inform us that he's not following Van Dine or Knox's rules of "fair" detective fiction and that... well, it's not a mystery that can be solved by us.
And then in the Chiru arcs the writer introudouces first a personification of the Knox rules, and then later a personification of the Van Dine rules.
At the end of the series, the answer becomes clear: the mysteries that Meta-Beatrice purposely set up (the first four arcs) are quite solvable, and for the most part follow Fair Play. The reason that the author said that he didn't want to give a straight answer is because we are never told what really happened on Rokkenjima. Most people thought that the whole 'not giving a straight answer' referred to the games themselves, which are just stories within the story, but it referred to the real events on the island. Confused yet?
Umineko also has a brilliant deconstruction of the Tsundere Moe in the third arc.
Mega Man X is a deconstruction of the Sentient Robot Heroes genre, if not the franchise. Unlike it's lighter predecessor, there is a major war going on between mavericks and maverick hunters, and many people, reploids and human (who are mainly off-screen) alike die. X4 is probably the biggest deconstruction of the franchise, if not X5. Zero, the main character's friend is speculated to be created by Wily and was made to destroy X. Also, he kills the brother of his love interest, who in turn, tries to avenge him, only to die as well, the war between the Maverick Hunters and Repliforce could have been avoided, and, as it turns out, Zero is the cause of the Maverick Virus and Sigma's Start of Darkness.
The fact that Zero is the cause of both the Maverick and Elf Wars can be seen as a deconstruction of Joker Immunity and Thou Shall Not Kill. If Dr. Wily was executed when he was arrested in Mega Man 6, Zero would never exist and so much death and destruction could've been avoided. But he wasn't, and some of his leftover projects came back and screwed things up for everybody.
Planescape: Torment is a deconstruction of RPGs. Characters in the gameworld comment on how adventurers are unwelcome in Sigil and how bad the main character looks and smells. It features a dungeon that deconstructs and ridicules the concept of dungeon hacking, the side-quests are... unusual to say the least. (Tired of these "Romeo and Juliet" quests that have you uniting annoying lovers? Planescape: Torment has a quest where you have to destroy a relationship.) Protagonist Without A Past is heavily subverted because NPCs remember your character while you don't (because he has several past lives' worth of amnesia). Experience is gained by remembering and regaining skills you already had, but forgot. The main quest is mainly about people you gave quests in the past, rats are powerful enemies, there are none of the typical D&D races, and an ANGEL is one of the antagonists! Oh, and there are only two swords in the whole game. (Your character can only use one.)
Tales of the Abyss takes a deconstructor chainsaw to every fantasy story revolving around destiny, screwing it and everything else that falls into the "Chosen One Fantasy" genre. Turns out that everyone in the world is assigned some role by a prophecy, but the "Chosen One" is actually a clone of the real one. This event threw the entire world's fate off-course, starting out with subtle alterations (like the Chosen One not dying like he was supposed to) and eventually winding up with most of the known world sunk beneath a poisonous miasma and a good portion of the world's population killed off and replicated. Even though the Big Bad says that "deviations are as nothing" in the eyes of this prophecy, we know better. Heck, towards the end of the game, the party actually winds up intentionally fulfilling part of the prophecy because they realise that there's no other way to save the world, but not long after the whole planet goes to hell. Basically, don't mess with fate.
The Tales series in general enjoys taking various RPG tropes and then brutally deconstructing them.
The Visual NovelCross Channel can be seen as a deconstruction of the numerous charecter archetypes found in anime in general and eroge games in paticular. Sure we have a cast full of tsunderes, cloud cookoolanders, emotionless girls, genki girls and what not. But where to do they all go to school? A special school for young people that cannot function in society.
Fallout: New Vegas features Caesar's Legion as one of the two main powers in the Mojave Wasteland. As the name suggests, they are essentially the Romans placed into a post-apocalyptic setting. As the progenitor of modern Western civilization, the glory of Rome is often seen through an intense Nostalgia Filter. You get to see some of Roman culture up close in this game, and it is ugly. There are probably no more complete monsters in the Legion than most other factions, but the slavery, misogyny, and sheer brutality of the Caesar's Legion makes it the black to the NCR's grey.
No More Heroes, especially the second game, seems to be a deconstruction of the ultra-violent type of game. Travis' rant toward the end of the sequel is basically summed up as "Even if the person is fictional, it's still a death, and you're kind of a bastard for forcing the killings to happen." It was even seemingly aimed at both Sylvia, and the player.
Meanwhile, most of the villainism of the series' Villain Protagonist, especially in the first game, comes from what would happen if a stereotypical videogame/anime geek retained their combat ability in the real world and lived life like they play games.
For one of Gamespot's April Fool's Day jokes, they have announced that Capcom has recently announced a new game called Mega Man Deconstructed. See 7:43 of this video.
Baldur's Gate deconstructs the well known idea that most of the world's problems tend to occur just as The Hero arrives on the scene. Due to CHARNAME's status as a Bhaalspawn, he/she is a literalDoom Magnet, so the fact that you seem to stumble upon a lot of trouble isn't coincidence, you are literally causing it through your own existence. Furthermore you are not the only Bhaalspawn out there causing chaos through existance. It doesn't help things that your father is the God of Murder.
A lighter example of Deconstruction would belong to SWAT 4, an FPS which objective is not shooting bad guys. Just plain shooting bad guys like in another FPS, in SWAT 4, does not net you a point. This game expects you to be a police officer, not an FPS character. To earn points (which needed to advance in harder difficulties), you must deal with the bad guys with non-lethal methods, and arresting them.
Pokémon Black and White deconstructs not just many of the implications of a Crapsaccharine World in the series that are hinted at through the Pokédex entries, but also decontructs the idea that everyone in the world of Pokémon thinks that it's a good idea to send kids and teenagers out into the wild to capture Pokémon, with Bianca's father feeling immensly concerned for her. Another part of it is the idea that no one bats an eyelash at Pokémon battles or no one thinks it's too violent with Team Plasma and N. Speaking of Team Plasma, the games also viciously deconstruct the concept of Moral Guardians and the validity of their intentions, as in essence that is what Team Plasma are.
Phantom Brave viciously deconstructs All of the Other Reindeer. The power of a Chroma (which is what Marona is) is, for all intents and purposes, necromancy, and as such it is widely regarded as a dark, unholy power, and people react accordingly to her. This isn't simply general disdain or mocking of her, this is real, genuine fear and hatred. Hell, listen to that woman who scolds her son for wanting to be friends with Marona in the opening chapter. You can literally feel the pure, unbridled barely contained rage she has at the mere mention of her name.
Air Pressure deconstructs the "do everything you can to build/improve your relationship with a cute girl" Romance Game plot. The protagonist actually starts out disillusioned about how much he depends on his girlfriend Leigh and wondering if he should break up with her, and having him ignore his doubts in favor of appeasing Leigh results in a deliberately Esoteric Happy Ending where it's all but outright stated that Leigh is actually a metaphor for drug addiction or abusive relationships in general and that the protagonist's decision that he can't live without her is not in any way romantic or healthy. Not only that, but the game's happiest ending is actually the one in which the protagonist breaks up with Leigh and feels genuinely happy about being independent from her.
Grand Theft Auto IV deconstructs its own series. Rather than glamourizing crime and criminals like its predecessors, it shows that most characters you meet in the game are broke, greedy and psychopathic because of falling into crime and the toll such a lifestyle takes on people is great. In addition, the end of the game where your cousin or your love interest is murdered, you get revenge but it feels hollow, and you spend the rest of the game alone and driving around.
Mass Effect 3 can be seen as doing this to the preceding games in the series and to other similar series (such as Halo) in that the heroic character upon which everything revolves isn't invincible but is being psychologically worn down by the pressure s/he is under.
And then there's the endings. So you're the Only Sane Man hero gathered a Ragtag Bunch of Misfits to fight against an Ancient Conspiracy who sweeps in and destroys all organic life for an apparently incomprehensible reason. What happens? Did you really think overloading the mass relays wasn't going to have horrible consequences, even if you stop the Reapers?
Virtual-ON, a mecha fighting game with characters that serve as nothing more than controlled mechas, is ultimately a deconstruction to the fighting games with characters who have personalities and backgrounds.
The first game juxtaposes typical US government posturing about freedom/democracy/"restoring stability to the region" with unsettling hints the Middle Eastern country was an oil-rich US puppet state, and contrasts the macho, cowboy attitude of the American grunts with a US Army tank named after a famous anti-war song, "War Pig", and levels named after anti-war movies like Apocalypse Now and Dr. Strangelove (which, like the American campaign, ends with massive nuclear devastation). While you're playing, the United States seems like a good guy championing peace and stability (obviously due to your player character being on their side), but the implication that to the other side it's an imperialist bully who can only be defeated by nuclear weapons remains. By the end, any player not under the sway of Confirmation Bias is left feeling like the game world is just a bunch of political structures throwing propaganda at each other to cover up the void where the truth should be. Sort of like real life.
The sequel goes even farther. It starts with a US task force performing three separate acts of unilateral action, but things sour when the Russian army invades the United States over a botched CIA operation that resulted in Russian civilians dead and an American soldier's finger on the trigger. But to the American grunts fending off the invasion, it's obvious they're the victims. The two sides, inflamed by nationalism, fight to avenge their countries with Patriotic Fervor unaware that that's exactly why a ranking American general purposefully botched the CIA op. In the game, the war is treated as a power fantasy between nationalists wearing the mask of righteousness. The human beings on the front lines, actually fighting for their country, are treated as disposable pawns by their leader.
The third and final game in the trilogy was made after Infinity Ward's founders were fired, and as a result it takes on a much more generic America Saves the Day tone, but even then it doesn't betray the anti-nationalist attitude. The United States never actually wins the war, nor is Russia treated as an irredeemable enemy. Moderates on both sides just get tired of conflict, and the end comes when American special forces rescue the Russian president from Russian extremist nationalists so he can order the military to stand down.
Katawa Shoujo deconstructs eroge Visual Novels, and quite a few romance tropes at the same time. In particular it deconstructs many 'girlfriend' archtypes found in this genre:
Lilly, the Proper Lady, and the Mary Sue. Nobody ever questions her decisions, so when she is forced into something she really doesn't want to do (ie emigrate, leaving everything she knows behind), no one is willing to call her out on it.
Hanako, the Shrinking Violet, genuinely hates being mollycoddled by Lilly and Hisao, and completely blows her top if pushed too far. She wants to expand her horizons and leave the trope behind.
Rin, the Cloud Cuckoo Lander, cannot make herself understood, and is genuinely frustarting to talk to as a consequence, leading to her generally being alone, as well as teetering pretty close to the Self Destruct button.
Emi, the Plucky Girl, cannot move on from the crash that killed her dad, though she can handle losing her legs just fine. As a result she keeps everyone at a distance. It can be argued her athelics obsessions is just a coping mechanism.
Shizune, the Spirited Competitor, is overbearing and often quite a pain to be with. She has no friends besides Misha as a result. She herself realises this, but can do little about it.