The Legend of Zelda, Zelda II The Adventure Of Link, and The Legend of Zelda: A Link to the Past have happy endings, But afterwards the games' endings range from bittersweet to downright depressing. A notable in-game example is The Legend of Zelda: Skyward Sword. Even though it takes a fairly balanced approach to the lighter and darker tones demonstrated in other entries, the first part of the game is very much on the lighthearted side. Even when Zelda falls down to the world beneath the clouds, nothing really feels at risk, and the game itself takes an optimistic approach to being able to find her. In fact, the only darker moments during the first section of the game are Link's brief nightmares of The Imprisoned, implying what's in store later on. However, when Ghirahim first appears (and for the remainder of his appearances), the game takes on a much darker tone. Sure, he's a classic example of Evil Is Hammy and can be quite entertaining when he wants to be, but he is very much a legitimate threat, and is downright terrifying and dangerous due to his disturbing lust for pain and death.
Any game of Dwarf Fortress. All of them. A lighthearted romp at the start, with seven cheery dwarves building their home in a seemingly cheery forest, plain, or jungle. And then it gets worse as time goes on, with dwarves dying off, being disemboweled, being flung against walls, until eventually your fortress explodes into civil war under constant sieges and deaths.
Ace Combat started off as a very early entry into the realm of 3D arcade style flying shoot-em-ups for the original PlayStation; though it was still at least somewhat more complicated than other competing titles and most of the gameplay elements that would define the series were already there, it didn't have much in the way of plot and was more or less a fairly straightforward game. By the time of Ace Combat 3, however, the flying and fighting aspects were framed by a deep and very well-developed story, which by the next title were often at best tangential in their impact on the player's actual missions and prone to focusing on the enemy just as much or more as on the player's side, as well as an increasing frequency in anti-war messages (odd in a game entirely about war, needless to say). The gameplay became more complex as well, introducing additional subtle realism tweaks such as more realistic aircraft momentum, and by the most recent title has had a corresponding effect on gameplay. The intro of the latest game, which probably tries a bit too hard when it comes to conveying the impact of war, embodies this trope and was duly featured on Unskippable.
Live A Live (pronounced Life Alive) as a result of the theme. When it happens depends entirely on your mileage and the order you play the chapters. Some are Lighter and Softer then others, at least two are terrifying, and if it's your first time you play in the chronological order without spoilers.
Earthbound is a silly, shiny, nice game with colors all around. Its sequel Mother 3, though...well, what do you think of jokes such as "I have good news and bad news. Good news, I found you a new weapon. Bad news, I found it stabbed through your wife's heart."?
While Mother 3 is certainly more of a Tear Jerker than Earthbound, they both have Cerebus Syndrome within their games. Earthbound starts with you dealing with cops who take pride in their ability to block roads and ends with you fighting a being of pure evil that is considered horror beyond measure by many players. Mother 3 starts with you in a peaceful, utopian village and ends with the main villain essentially owning the entire world.
The sequel to Beyond Good & Evil looks to be far less cartoony and both teasers available indicate the game will take place in a city in the middle of the desert. Sounds familiar.
In Final Fantasy IX, you start with a bunch of thieves/actors kidnapping a rebellious princess and a kid who goes to watch a theater play. The first 7 or 8 hours of the game (especially in the brilliantly done French translation) are lighthearted and fun. Then, the thieves'/actors' hometown is invaded, the rebellious princess sees the death of her mother and watches her kingdom getting nuked, the whole world comes close to destruction, and the little cute kid of the intro gets to deal with his own mortality.
Suikoden Tierkreis starts with the main character living a mostly carefree life in his little village, cue a militaristic cult appearing. The main character decides then to stand against it, while remaining mostly optimistic; cue the multiverse collapsing.
Dragon Quest V begins with the main character as a child, journeying with his dad, occasionally going off on his own or with a friend on adventures straight out of Tom Sawyer, The Chronicles of Narnia, or George MacDonald's fairy tales. Then, while trying to rescue a bratty prince, he watches his father get killed, and is sold into slavery, setting up the main plot of the game.
Dragon Quest VII starts also with the main character living a carefree life in a fishermen village, and the "DQ humor" still drives most of the storyline. Then the first chapters of the game proper start, but, while more dark, they remain mostly into the "dungeon of the week" routine and the story keeps many humorous moments. Then, little by little, each small chapter gets more and more tragic until the conclusion.
Tales of Phantasia starts with two main characters hunting, then it turns into a vendetta story, then into a world war, then into a conflict to save the human race, than the heroes discover that Dhaos was the good guy all along. The comedic elements of the game's beginning are of course diminishing through the story.
This is the entire series. Nearly every game can be summed up as "naive swordsman goes out on minor errand and stumbles on a plot to end the world". Ruca of Tales of Innocence is currently the record holder, wandering into the plot of the game while hanging around town to play with his "friends".
Performed rather well in Tales of Graces with the playable prologue. We're introduced to the young kids having fun with their new friend, meeting a new important friend...and then quickly watching as their new friend sacrifices herself before their very eyes with nothing they could do and (while they didn't know it yet), their other new friend was possessed by Lambda. The result? Four to five out of the seven playable characters have a rather Dark and Troubled Past. (Not counting Malik, who has a different and unrelated Dark and Troubled Past)
The difference between the first act of Tales of the Abyss and the third act of Tales Of The Abyss is the difference between accidentally destroying a city of 10,000 people and Jade lightening the mood by snarking at you, and voluntarily sacrificing 10,000 replicas including the protagonist, all of whom are still mentally children, while Jade wishes he could go back in time and kill himself as a newborn because everything in the game is his fault, including this incident, because he suggested it. Compared to Tales of Symphonia, the last American release, the game itself is pretty much Cerebus Syndrome applied to the series as a whole, though the trend is reversed with Tales of Vesperia.
Fire Emblem: Path of Radiance, while not really "comedic", is fairly light at the beginning, with a teenage mercenary learning the ropes of his job against small bandit bands and under the careful watch of older fighters. By the end of its sequel, the plot looks like an adaptation of Berserk with slightly more colors.
Most Fire Emblem games tend to follow the "let's put these mean, ugly bandits in their place -> oh crap the world's gonna end" formula. But the one game in the series that really pulls the stops is, without a doubt, the fourth one, Genealogy of the Holy War. It starts off with a young lord repelling an invasion by a neighboring kingdom with his knights and some noble friends, going off to battle in his country's name, making new friends and losing others along the way, having his girlfriend/wife kidnapped, being framed for a murder and seeking to speak to the king to clean his name. Sounds like a pretty standard plot for a medieval fantasy game, right? Not when chapter 5 comes in, it isn't. While hints are given along the way that some seedy stuff is going on, nothing compares to what happens there.
Grandia starts with two kids doing their usual antics in their hometown and dreaming of adventures that are, quite obviously, way above their level. By the end of the game, one of the kids, Justin, has turned into a badass by being punched in the face, repeatedly
Arc The Lad starts with a mostly light hearted storyline, with three of the seven Player Characters being comic relief. Then Arc 2 comes along, and it becomes darker, and darker, and darker, and darker... At the end, Gogen is still cracking jokes and Poco is still a klutz, but it is hard to notice the comedy when you failed to stop the apocalypse and lost your main couple.
Chrono Trigger was, at some point, about going to the fair and having fun. You even meet a cute girl. Her pendant causes time travel, and wacky times are had by all. Even after you get tried and thrown in a cell for a few days, things are still lighthearted. Then you leap in the nearly dead future and see a recording of how the world ended...
The sequel, Chrono Cross, starts out rather okay, but after mid game, the hero gets his body switched with the bad guy, and the plot goes complicated and dark. Worse, the story's tying up with Chrono Trigger by destroying every happy part of the prequel. Crono, Marle, and Lucca are likely to be killed shortly after "Trigger" ends, and Schala is turned from a heroic sacrificial woman to a Woobie, Destroyer of Worlds.
Zig-Zagged in Kingdom Hearts. While the first games released chronologically were pretty lighthearted, Days and Birth By Sleep are actually a lot darker in general, what with finding new characters who were Doomed by Canon and finding it all set in a Crap Saccharine World and a couple malicious villains. The games even started off pretty lighthearted, too.
Advance Wars had this; the first game was sort of up beat, with you fighting it out with the clear-cut bad guys. Second game, still upbeat, but the villain is somewhat more... unnerving. Third game, the villains are sucking the life out of the planet, there's few signs you can do anything to change this, and you choose at the end whether the Big Bad lives or dies. The latest one is set in a post apocalyptic wasteland where the NPCs in the campaign tell you to leave the civilians behind and the first fight you have is with piratical raiders.
And the big bad? Strum wanted to take over the world. Von Bolt wanted to live forever. Caulder, on the other hand, conducts experiments on what's left of humanity.
The flash game Viricide goes, over the course of the paragraphs that pop up between the 17 waves, from jokes about an AI's malfunctioning double entendre system, to said AI explaining that her programmer was taking depression meds while working on her, and one day told her he was going to solve all his problems by taking all the pills in the bottle at once instead of taking them two at a time. She never saw him again, but hopes what he did made him feel better.
She also goes from referring to her programer as "my programmer" to calling him "my father" and "Dad" and she asks you to disable her "emotional core" which gives her a personality.
The first map, Nacht der Untoten, was really just four AFGNCAAPs holed up in a building under siege by unlimited hordes of zombies.
The second map, Verruckt, was more of the same, with Perk-a-cola machines and electro-shock defenses. And the EVIL teddy bear.
But the third map, Shi no Numa, not only features four well-defined characters, but has lots and lots of Easter eggs hinting to the origins of the zombies, and most of all, This.
Der Riese, the next map continues this somewhat. To some extent, less dark looking than Verrukt, but it's where the zombies and hellhounds were created, apparently after experimentation on live patients and dogs, according to these radio conversations and Easter eggs. It's also got things like teleporters, rounds with both dogs and zombies, and possibly the origins of both of them.
Conkers Bad Fur Day starts off, and plays as, a ridiculously over the top and bizarre adventure bordering on satire. However, starting from the Spooky level, the plot quickly becomes darker and darker, ultimately culminating in one of the bleakest endings in video game history. In comparison, the first game in the series was an E-rated Game Boy Color game.
Pokémon. While world-influencing and universe-influencing events were beyond the scope of the early games, Team Rocket tortured people, killed a Pokémon, held people hostage, took over companies and buildings (terrorism), attacked (and recruited) ten-year-olds, and promoted gambling. They were on a much smaller scale but it is arguable how much heavier the plot really got, if at all. Sequel Escalation is definite either way.
Team Galactic does all of that stuff too, but they also try to suicide bomb Celestic Town.
The anime had a different form of this than most. While it usually doesn't get really dark outside of the movies, the series goes in the opposite direction of its Denser And Wackier first season. Then by the Diamond and Pearl seasons, Team Galactic and Pokemon Hunter J made some episodes a lot darker. And now they're in Unova, where the Terrible Trio suddenly Took a Level in Badass, and our heroes will presumably fight Ghetsis at some point...
The Pokemon Mystery Dungeon series. The Rescue Team games had their dark moments but were fairly consistently upbeat throughout. The Explorers series start off their plots more or less in line with the first games' in terms of tone, but almost immediately after the halfway point drops, all traces of comedy vanish, setting the stage for an incredibly morose plot.
And the latest installment Gates to Infinity took this Up to Eleven starting with you and your partner building a pokemon paradise to having to stop Kyurem and his suicide cult from destroying the whole world.
Telltale's Sam and Max games have always been darkly humorous adventures without a bit of seriousness. Then The Devil's Playhouse began. The comedy remained, but a lot more emphasis was placed on the narrative. The series' Crapsack World stopped being played totally for jokes, episode continuity became much tighter, and the tone became darker and darker, leading all the way to the finale and Max's death.
The first Portal game touches on this. In the beginning GLaDOS's jokes seem unintentionally funny, but as the game progresses the player finds out it/she has a serious (and homicidal) personality disorder. The game rapidly descends from an upbeat puzzler into life-threatening drama. However,it still manages to be quite funny.
Parodied and subverted in Recettear. At the end of Obsidian Tower, Griff reveals his plot to restore power to the demon race, which would wreak havoc all over the place...then Recette mocks his plan for being really cliche.
The Broodwar addon did this to Starcraft, although the Starcraft universe wasn't a very cheerful one to begin with.
Heck, the first one had a bittersweet ending, with the Overmind being destroyed and Tassadar dying. Broodwar had the UED, Dominion, Protoss and Raiders combining for an epic battle against Kerrigan that we knew they would win. Then Kerrigan slaughters them all.
Happened to a certain extent in the Fallout universe. Fallout 2 was full of wacky gags and fourth-wall-breaking humor (an item that only be gained by having one of your stats permanently reduced includes "If you're reading this, you're probably going to reload," as part of its description). In comparison, Fallout 3 is a very serious game that focuses on easing the brutality of a Crapsack World.
Custom Robo doesn't even try to take itself seriously. Villains are mostly comical, the story lighthearted, and not too much hint of the events to come. Then comes the Info Dump with two separate save points...and it all goes downhill from there (granted, you can invoke some humour by picking the funny dialogue options. It's just not played up automatically).
Brothers in Arms Hell's Highway follows this trope quite well. Not counting the In Medias Res at the beginning, the game starts pretty upbeat, with the squad bouncing across the Dutch countryside in their jeeps. There are a few darker moments, like a part with a priest getting killed by an artillery shell, Baker's flashbacks, and the bloody fighting, but it manages to bounce back after everything's said and done....until Eindhoven. After that, things begin to spiral downwards.
This is pretty much the textbook description for Operation Market Garden.
Key Visual Arts games do this deliberately, starting off with happy, Slice of Life gameplay revolving around a guy and a bunch of girls in a school and then slowly bringing in the drama (and later, extreme drama) as you move onto a route. (Things always work out eventually, though.) Little Busters is particularly notable - most summaries seem to be along the lines of 'A young boy is saved from depression from a group of friends who get into all kinds of mischief together!' as though it's just a fun, relaxing, comedy game. It isn't.
The Zookeeper puzzle game's apparent Excuse Plot is about a zoo keeper who has to keep order in a zoo in which the animals are rebelling against the strict, evil zoo curator, who tends to comically mock the keeper in the game over screen. If you play well enough, you learn the backstory: the curator and his wife once wished to create the greatest zoo in the world, but then she died in an accident, which he felt terribly guilty for. In his grief, he began to hate the zoo, until the zoo keeper's (his son) hard work makes him see the error of his ways.
Team Fortress 2. The original concept was "two teams kill each other in the desert" with basically no plot. Since then, the story has expanding through manuals and trailers to create what Valve describes as one of their most labyrinthine stories. At this point, the story involves everything from a genius-making material called Australium, a world-hat economy, an evil magician and an implacable army of robots.
Indie game OFF gets hit with this hard. It starts off with a man called 'The Batter' fighting ghosts in a relatively quirky world and it quickly goes downhill from there.
While all the Baldur's Gate games contain grim elements, the ratio of comedy to tragedy decreases with each successive game. The first game had a Belt of Gender-Changing, an repeatedly-exploding ogre, talking chickens, comically-depressed elves, and Minsc. Most of the humor in Shadows of Amn comes from the dialogue of either Minsc or Jan Jansen. It also upped the whump-factor with such events as Irenicus' physical and psychological torture of Imoen, the torture and implied vivisection of Khalid, and the player-character's Bhaal-spawn nature breaking free. Most the NPCs you can add to your party come with tragedy pre-installed ( Aerie, Valygar) or pick some up in-game ( Minsc, Jaheira, Jan Jansen, Yoshimo, Imoen). In the expansion-and-series-resolution, nearly the only moment of comedy is an imp artificer implying that he gets his recipes from denzien of Hell, Martha Stewart.
A fan-mod was specifically written to address the change in tone between the first and second games with the tagline "When did we stop having fun?"
The indie game Eversion does this. The game starts off as a cutesy 2D scroller with colorful environments and non-threatening enemies. As you use your Eversion power more and more, the game starts taking a dark turn. Environments are gloomier, the music changes, and enemies seem noticeably depressed. Eventually, the game starts to look more like a nightmare than a happy platformer. You start to realize the effects your power has on the world around you, but you can't stop using the power if you want to progress.
Kingdom of Loathing, of all places, features this with content in the Bonus Dungeon "The Sea" that gets rather dark near the end. The Sea starts out featuring the usual assortment of multiple bad puns and cheesy pop-culture references... then you get to The Caliginous Abyss, which is populated with monsters that wouldn't look out of place in Eversion. Down there, you eventually find Mom Sea Monkee, who's gone completely over the edge and has apparently been touched by dark magics, causing her to give you one of several unsettling buffs if you talk to her after rescuing her. Little Brother Sea Monkee seems reluctant to talk about his father, but you do eventually find Dad Sea Monkee... if you're persistent enough to defeat both Bonus Bosses Shub-Jiggawat and Yog-Gurt, with all six core classes, and assemble six of the seven pieces of the Clothing of Loathing, you'll find Dad... almost catatonic, and hooked up to a bizarre machine that's super-charging him with dark, unknowable powers from the depths of the cosmos.
NieR doesn't exactly start off light-hearted (the prologue, especially), but in the first half of the game things generally go well for the protagonists and the people they're trying to help, and even when it doesn't work out so well there is a lingering feeling of hope and optimism. However the game has a marked shift in tone in the second half, starting with the main character's daughter/sister being kidnapped by a super powerful Shade. The game then proceeds to get darker and darker, especially towards the very end and on subsequent playthroughs, where you find out that the shades are sentient (in fact, they are the original humans of the world) and the majority of your actions in the latter half of the game involved striking down people who were largely innocent. You were basically a mass murderer and by the end of the game you've doomed humanity to extinction.