Lots of interesting things are going on in the series' Myth Arc: Mind Screws, wildconspiracies, unrevealed Love Dodecahedrons, an Ontological Mystery, and the odd bit of Applied Phlebotinum or two. Sometimes the setting itself is just plain crazy, to boot. It's a Long Story, and there's far too much to explain in the series pilot.
Solution: ration out the information about what's going on with an eyedropper, and let the viewers scratch their heads about it until much later on. Welcome to the Jigsaw Puzzle Plot.
At its best (and with a sharp audience that's well-prepared for it), the series can become an interesting intellectual challenge that generates hours and hours of Fan Wank, Epileptic Trees and watercooler discussions, and creates memorable moments as connections between seemingly minor or unrelated details fall into place, revealing illuminating insights (see Wham Episode). At its worst, the series becomes an incomprehensible Mind Screw ruled by The Chris Carter Effect, patched together by the occasional Ass Pull. Some writers may claim some of the latter effect to be intentional; that some mysteries are never solved. However, the fact remains that if you give viewers a mystery, suspects, and clues, then don't tell them whodunnit, don't act surprised if they get pissed at you afterwards.
Anime does this quite frequently, and even series that don't explicitly try for a full Jigsaw Puzzle Plot will frequently hold back explanation of a few scenes in the Pilot until Mr. Exposition has a chance to talk about it without seeming overly Anvilicious.
Very common in arc-based mystery or espionage series, where what's going on is supposed to be mysterious. By its nature uses several Driving Questions right at the outset. Expect many Reveals. Can often become a Kudzu Plot if the pieces of the puzzle don't quite fit together.
Not to be confused with the kind of plot that involves failing to escape deathtraps.
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Anime and Manga
Attack on Titan throws several curveballs regarding the nature and motives of Titans within the series, most of which just raise more questions than provide answers.
Star Driver, from the same writer as Utena, also fits very well.
Noir fits this pattern admirably, despite its (relatively) short run. Early episodes will frequently contain multiple flashbacks with no apparent relevance to the event which triggers them. Most of these connections are eventually revealed, however.
Due to artistic reasons or whatnot, it's actually impossible to piece together some of the puzzles in the Series on it's own, therefore REQUIRING third party material to be explained. Annoyingly enough, the Third Party Material itself also adds MORE questions which are not resolved, which is why Evangelion is more of a Kudzu Plot.
Texhnolyze can be a very tricky story to piece together, especially considering all that's going on between the Raffia, the Organo, the Class, and the shared history that ties them all together. It's very tight-lipped about its secrets.
Gasaraki is quite similar, except instead of giving you a new puzzle, it pours gasoline on the old puzzle, then drops a lit match on it, then doses you with either very good or very bad hallucinogens, depending on how drunk you are at the time.
Red Garden might be the all-time king of this and still make sense in the end. The viewer is given information at the same pace as the protagonists, which means one has no idea why ANYTHING is going on up until three-fourth of the way through the story, when the protagonists are finally trusted enough to be told exactly why they are fighting for their lives. You can, of course, figure it out a bit earlier then that, but up until then, you're only seeing a small portion of the puzzle.
RahXephon The anime TV series version of it was pre-planned as a jigsaw plot, with hints that become obvious on a second viewing.
And the final puzzle piece comes after the closing credits of the last episode (so make sure to watch all the way through them, if you haven't finished the series!), thus practically necessitating a rewatch with the new info in mind.
Much like RahXephon, Wolf's Rain has a tendency to keep many of its secrets well-hidden in the background beneath several subtle hints and layers of symbolism. You really have to be paying attention to figure out what the nobles actually are.
Get Backers loves this trope, explicitly citing the "puzzle" simile every chance they get. There's a twist, though: while it starts out as a straightforward piece of advice- "don't do anything stupid until you figure out exactly what's going on"- it turns out that many superficially unconnected plot threads are in fact pieces of a much larger puzzle.
Mobile Suit Gundam 00: One example suffices; the primary design for the Innovators, the main villains of Season 2 can be seen in contextually-relevant background scenes in Season 1, specifically on Kinue Crossroad's desk.
Kekkaishi and all the stuff relating to Karasumori and the Urakai.
Eden of the East. We get to see a lot of slice of life, romance and occasional comedy all while knowing that the story has a much more complex and mysterious plot, setting and back story. We'll only get to see that piece by piece.
One Piece, especially between story arcs where we receive glimpses of the bigger world outside of the Straw Hats adventures. Slowly but surely the details of the overall myth arc concerning the One Piece and the Lost One Hundred Years have been coming together and still have some way to go.
Pandora Hearts, especially regarding the Tragedy of Sablier, Pandora, Abyss, Will of Abyss, and almost everything, really.
Kara no Kyoukai due to the first four of its seven parts being in Anachronic Order. Those unfamiliar with Tsukihime (which Kara No Kyoukai was a prototype of) would have absolutely no idea what's going on until the end of the third movie.
Princess Tutu. Stuff that isn't revealed until much later (some up to near the end!) are hinted at in the first few episodes, but it takes a while for everything to fit together. Also, every episode has at least one small thing revealed that's important to the plot, even if it seems like filler. Mytho himself could be seen as a representation of this, since we only learn his personality one "piece" at a time.
Steins;Gate does this. Since the story revolves around Time Travel and a conspiracy, it's only to be expected. A lot of stuff is thrown at you in the first episode, and nothing becomes clear until the last episode when all of the pieces are neatly placed together.
The manga version is somewhat like what would happen if you're given a few small pieces to a puzzle at a time, only for the person giving you the puzzle realizing they're low on time and dumping the whole box of pieces out at you at the last minute. Thanks to some of the exposition being rushed, some things that are only barely hinted at seem to come out of nowhere (like the demons being aliens) and some things are touched on so quickly it's easy to miss them (like Satella and Fiore being half-demon or Joshua and Azmaria being married in the epilogue).
The anime version reveals things a little more smoothly, but thanks to its Gecko Ending a lot of the foreshadowing to things earlier in the manga isn't touched on again in the anime. Basically, in this version you're given half of one puzzle, and then pieces of another puzzle that only fit together if you force them, with some leftovers on the side. This leads to some things appearing in the series that don't make much sense, like the demons' advanced technology.
The Big O is like one of those advanced jigsaws where every piece is the same color. By design, some of the pieces never do fit (the rumors that this is because of Executive Meddling are false; the "original" ending to the second and last season was only slightly more coherent).
Amatsuki, particularly concerning the backstory and the real world timeline.
The anime version of Trigun, in stark contrast to the manga, has a tendency to focus very heavily on the human elements of its story while confining many of the other backstory details to subtle cues that might go unnoticed on a first viewing.
Grant Morrison writes a lot of these. It's not always a bad thing, though, just seems to be his style.
100 Bullets slowly builds on its background Myth Arc one piece at a time. The Minutemen and the Trust? Those names aren't even mentioned in the first few arcs.
The Sandman. Through all the stories the characters mix up slowly and in ways that aren't initially obvious and characters that were initially in two panels as a mention become major players later on.
Elephantmen tells it story from multiple character perspectives and sometimes out of sequence.
John Byrne's run on She-Hulk worked like this. Small two page snippets would later contribute to the storyline. The Greek Gods arguing about Cupid being able to make someone in love with anybody else and then combining this with a conquerer from the future just arriving, for example.
The Firefly fanfic Forward has gradually hinted a far deeper and more complex plot as the series progresses, revolving around the Academy and their goals regarding creating psychics like River. Hints and clues as to what the Academy is really doing are dropped all throughout the story.
An author example is Kalash93. Many of his stories connect together very subtly, and attentive repeat readers will spot the connections. Not all the pieces are together yet, and what is there is not always told in order.
Cloverfield uses this big time. You won't get the full story in the movie at all. Looking into the ARG explains somethings and gives a few implications. By the end of both your left having to figure out how a giant monster, a bunch of big parasite things, a Japanese corporation, the government, and an anti-corporate terrorist who seems to know something about the monster are all tied together.
Spoofed in Hot Fuzz, where Nicholas Angel's investigations about a series of murders bring together all the clues in a complex web of intrigues... except they didn't really matter and the real reason for the murders was far simpler and stupider.
The 1972 version of Солярис (Solaris) is an example of what can go wrong when Jigsaw Plot is mixed with adapting from book to film. The film based heavily on a novel which heavily relied on the narrator giving massive information dumps to give backstory and explain things. Given that much of the film adaptation is based on the actions that take place in the novel, but is bereft of any narration, meaning that things which made sense (or at least slightly more sense) in the novel, went completely unexplained in the film without buildup, exposition, or closure. Many plot revelations and pieces of characterization were changed to something very different, making the film hard to approach even for those who have read the book. The film also adds several scenes not found in the novel at all, which are quite trippy, leading to a film which has disturbingly large chunks of its running time occupied by Big Lipped Alligator Moments.Mind Screw and Gainax Ending do not even begin to express how weird the whole thing is.
The Wheel of Time. To understand the plot isn't difficult, despite the number of main characters. The confusing part is truly understanding everyone's reactions. It requires a great deal of knowledge about both the plot and most characters' personalities and roles.
P.C. Hodgell's Chronicles of the Kencyrath wherein there's a fully fleshed-out fantasy world with its own ecosystem, magic, and theology. The main character, Jame, is (mostly) aware of how the world works, but doesn't explain any of it until relevant. Furthermore, she has only vague memories of ten years that passed where she didn't age. What she knows of the world is largely revealed by the second book. How the world actually works is still being revealed as of the fourth book.
The Dresden Files. We're gradually learning things about Harry, his universe, and the main Plot that surrounds him.
William Faulkner's short story A Rose for Emily is comprised of five parts which are mostly out of order. For those who don't pick apart and reassemble the events, whether Emily killed her beau, and why, is a perplexing matter. The fact that the narrator (implied to be the townspeople) has a severely limited understanding of Emily's personal life and occasionally relies on conjecture to guess at her actions doesn't help much either.
The Fall Of Hyperion is a continuous downward spiral into a labyrinthine web of conspiracies within conspiracies on a cosmic scale.
The Newbery award-winning novel The Westing Game's title puzzle/scavenger game is just one Mind Screw after another.
Otherland, a Post-Cyberpunk novel series by Tad Williams, takes an achingly long time to introduce all of the elements of its Kudzu Plot to readers, and even at the end, forces people to fill in some of the blanks themselves.
Rant by Chuck Palahniuk is told from several different viewpoints all at once (often contradicting each other) by way of having the side characters interviewed after the fact. SEVERAL different ways of putting this puzzle together are possible.
Warrior Cats, mostly in Power of Three and Omen of the Stars. We're slowly but surely figuring out the origins of the three, as well as The Dark Forest and StarClan among other things.
Holes just barely qualifies, as it has two subplots which are not connected to the main plot until towards the end of the book.
Twin Peaks. However, it was prematurely cancelled, with the ultimate effect that the Jigsaw Puzzle Plot was comprised of seven different jigsaws, each with half its pieces missing, along with several blank pieces that fit anywhere, plus two chess pieces and the little pewter boot from a Monopoly set.
The X-Files didn't start out this way, but Gillian Anderson's pregnancy early in the series forced the writing staff to get very inventive, and the show's near-legendary Myth Arc was the result.
Alias. In this TV series, the mythic arc takes a shadowy backseat to the "everyday" spy dramas that Sydney faces.
LOST. For the first half of the show, the writers had the task of constructing a character-driven narrative within a dense mythological framework without knowing how long the series would last. Many story threads were introduced right off the bat, but there was no way of knowing whether each phase of the story would have to last ten episodes or several seasons. Trying to avoid dragging plots beyond their natural shelf-life and putting the next piece of the puzzle into play is a difficult balancing act for a television network's cash cow. This along with certain other events caused many Aborted Arcs to occur.
Star Trek traditionally prefers standalone stories (even Deep Space Nine only planned so far ahead); however, the third season of Enterprise was a full-scale Jigsaw Puzzle Plot.
While each episode had its own self-contained story, the overreaching arc in The Pretender, with its questions of Jarod's family and who was in charge at The Centre, was a Twin Peaks style Jigsaw Puzzle Plot.
The backstory of Power Rangers Mystic Force. You always get bits and pieces, some of which don't seem to fit with the rest, and it doesn't all fall into place until 2/3 of the way through. This is one of the major differences between it and its Japanese counterpart Mahou Sentai Magiranger, whose only secret is Wolzard's true identity. We learn the answer to that and trade it for one more mystery: "your mom's still alive; ask the next set of bad guys how that can be and where she is now."
This is unusual for both Power Rangers and Super Sentai, but their Darker and Edgier sister series Kamen Rider has long been this way. At the beginning of a series, the hero gets his powers and monsters are attacking and... that's about all we know. The monsters' methodology (and in Kamen Rider Dragon Knight, the number of rival Riders) make filling an episode easy even with a lot of what is going on unrevealed. The events that set it in motion and the final plan of the enemy are filled in piece by piece. Even the more lighthearted Kamen Rider Den-O doesn't introduce the Big Bad until the series is 2/3 of the way through. Until then, all we knew is that the Imagin did what they did because someone or something was whispering in their minds' ear. Mind you, this goes strictly for the 2000s Revival and after.
By Season Two, Supernatural got pretty good at this. You usually had an episode furthering the FBI Arc ("Nightshifter"), then a Monster of the Week episode ("Houses Of The Holy"), then something to do with Sam's destiny ("Born Under A Bad Sign"), then a Breather Episode ("Tall Tales"), all the while dropping hints about the boys' usually-damaged mental states.
Each season of Australian drama Sea Patrol does this.
The first series builds up a mystery involving a mysteriously poisoned marine biologist, a freighter captain, a bag of contaminated crabs, the fishermen who caught them, and a crate full of water bottles. It all comes together in the season final, when Captain Gallagher is revealed to be manufacturing a biotoxin to sell on the black market.
The second series, subtitled "The Coup," builds up to a coup d'etat on a fictitious Pacific island, involving an Australian businessman and a group of Eastern European mercenaries. It's not done quite as well as the first, because any viewer can tell that Walsman will be behind it from roughly the second episode. Surprisingly, individual episodes in this season are on average better than in the first, but the mystery is badly handled.
The Shadow Line does this, as it has many seemingly disparate plot points that only fall clearly into place in the final two episodes.
Up to eleven with the fourth season of Arrested Development which exploits the fact that all 15 episodes were released at once with each episode being A Day in the Limelight for one character catching us up on what happened with them in the years after season 3 which leads to many overlapping storylines and setups to jokes that sometimes are not paid off for as long as 10 episodes.
Square Enix's RPG Chaos Rings is built on this trope. Each playthrough features one of four different parties, whose stories are all interrelated. Only once you've played through each of their paths does the overarching plot come together.
With the addition of the bordering on Mind Screw ending of Brotherhood, the Framing Story of Assassin's Creed definitely qualifies for this now. Ubisoft were meticulously vague with just about every sentence said, giving the player bits of evidence and conspiracies that either seem to contradict each other, or seeming have no relevance whatsoever. Not to mention the player has NO IDEA if said sources of information can be trusted, if everyone secretly has an ulterior motive, or if they're just being overly paranoid about things. "Nothing is True, Everything is Permitted"... more like "Believe NOTHING, expect EVERYTHING, but don't expect to know how it all fits together".
Doom 3 did this quite nicely with its audio logs, video disks, and emails. Plus, it also did wonders for making players actually get the plot by placing important information such as codes in with the plot threads.
Horror-themed video games seem to be fond of this. Clock Tower 1 and 2 (by JP numbering), Silent Hill, and Resident Evil all use this to varying degrees; the Clock Tower games take it to the point of Mind Screw, and the comparatively more straightforward third game might actually be a response to this.
The Legacy of Kain series, with plan upon plan, a whole cast of Chessmasters, of varying levels of ability and success, and a(n un)healthy dose of time travel....it becomes quite a headache to keep it all in mind.
killer7 sets the puzzle pieces in front of you, takes a handful away, and leaves you to assemble the rest.
Oracle of Tao: Ummm, maybe it's better to visit the site page. It's a bit difficult to example all the many plotlines.
The World Ends with You to some extent. However, it actually lets you unlock special messages to clear up some parts after the main story is over.
The Kingdom Hearts series. It rations out the information just enough that all the WMG and Fan Wank can start to make sense if you aren't careful.
Birth By Sleep is probably the best example, as you have to play the game three times (each time as a different character) to piece together the entire story, plus gather all the "Xehanort Reports" that explain (as best they can) the more confusing details.
Dream Drop Distance gives the big picture by including detailed summaries of all the previous games in the series, and shows how all the plots are tied together.
Odin Sphere. The story prior to Armageddon is spread throughout five books telling different parts of the story from the perspectives of five different characters. Trying to keep track of everything - such as who does what, what goes where, and when what happens - can be extremely frustrating, especially if you're trying to figure out how the ring Titrel is passed from person to person or how each character pursues their agenda. It doesn't help that the game often jumps through hoops of And Now for Someone Completely Different. Thankfully, the game provides a cinematic theater organized into a comprehensive timeline to properly keep track of everything in a chronological order.
Jon Ingold's text adventure All Roads is rare example of a computer game that pulled this off with only a few hours of gameplay. The full plot involves possession, body switching, and anachronic storytelling. And then there was The Muldoon Legacy series by the same author, which added a healthy dose of science fantasy.
Similar to the killer7 example above, Suda 51's The Silver Case series follows this trope. It begins with Moonlight Syndrome, in which nearly everyone dies, moves on to The Silver Case itself, in which the only detective investigating the events of Moonlight Syndrome is murdered, and then moves on to Flower, Sun and Rain, whose plot is too complicated and fantastic to explain here.
By the way, one of the characters from Moonlight Syndrome makes a cameo in killer 7. The two boys with the adult voice are Mitra. And that game never came out in America. Suda 51 is doing this for his own sick amusement, isn't he?
The Siren games are designed like this, challenging the player to piece together the truth from the various character scenarios and the many archive items that can be found. Even then, the game outright hides certain pieces of the puzzle from you; for example, the first game never shows the scene where Kei Makino is murdered by his twin brother, who assumes his identity and effectively replaces him in his scenarios.
While Deus Ex's main story is pretty straight, the backstory is hidden in pieces in various in-game media this way.
In fairness, by the time you'd reached the end of the game, it was pretty easy to forget some of the details. The game makes more sense each time you play through. All the subtlety also tends to make the stuff the story beats you over the head with that much more overwhelming.
Final Fantasy VII before it wasn't any better; only by the end of the game will you most likely understand everything that has gone on before, then a replay is recommended. It's possible to skip all the optional scenes that explain the backstory, and without them, it's practically a different game altogether.
The protagonist of Prototype has a Cannibalism Superpower, so he learns the backstory by eating people who have memories connected to it. This is made more complicated by the fact that few of these people fully understand the situation (and according to one memory, some of them were deliberately given false info once the higher-ups figured out that any real info might get back to the protagonist.) The result is a bit confusing, to say the least.
Half-Life has the basic story of "mad science allows extradimensional aliens to conquer the Earth." Beyond that, you have to notice newspaper clippings in the game, keep your ears open for off-hand references in dialogue, and pay close attention to how your alien allies speak. It can be frustrating, but the alternative could have been a scene in Half-Life 2 where Gordon Freeman was locked in a room with an actual slide show of exposition.
Even then, even if you are paying very close attention throughout much of the game, if you only play Half-Life 2, then expect to still be pretty damn confused and ignorant regarding the overall plot. Much helpful information is not given until Episode 1. That's right; HL2 makes you wait for the next game to clue you in on massive sections of the plot.
BlazBlue: Calamity Trigger. The main story is told piecemeal through every character's Arcade and Story Modes. Some players might find making a chart or a table handy, 'cause it gets complicated. Then, once enough pieces are revealed, it becomes simpler in a satisfying way.
Unfortunately, because it's a Fighting Game, a search for information on how to use the characters often ends with a plenitude of spoilers, which may not be major (fighting game) but it can ruin the satisfaction that figuring it all out near the completion of the story provides.
Heavy Rain. Let's just call it a mystery with multiple player-determined characters and paths and solutions but set answers.
While The Longest Journey had some elements of this trope, its sequel, Dreamfall, goes full-hog with it. So many pieces, and not enough game to cover them with.
The Professor Layton series, of course— they're point-and-click adventure games with mystery plots, so it's pretty much to be expected. The games even go so far as to have a screen of unresolved plot questions, with each one checked off as the details are discovered.
Mass Effect is heading for this. The main plot is fairly straightforward, but if you do loads of sidequests and talk to people a lot little details start cropping up - e.g. in the first game, Wrex can tell you a story about an asari mercenary he knew and fought with. In the second, an asari you meet (Aria T'Loak) unknowingly implies that she was that mercenary.
The series more or less ended up falling victim to The Chris Carter Effect by the third iteration, though, as multiple plot threads that had been dangled for the player ended up dropped and/or ignored outright, such as the abovementioned story about Wrex and the mercenary. A popular theory is that massive writer turnover at Bioware (including the departure of one lead writer, Drew Karpyshyn) is to blame for this, at least partially.
Hotel Dusk: Room 215 does this as well. You yourself are looking for your former partner Bradley, and as you talk to the residents of Hotel Dusk and learn their stories they begin to slowly interweave and overlap with yours and each others. By the end of the game you've found peace for yourself and everyone else in the hotel, if not resolved their problems.
Star Control II just throws you into a huge starmap with no set objective aside from a vague "become powerful enough to defeat the bad guys", and the only information you have is 20 years out of date. It's up to you figure out what's going on and what you need to do from the bits and pieces of information you get from the aliens you encounter.
Nier, strangely jumping ahead 1312 years after the tutorial and only giving hints as to what happened in the interim. Nothing is as it seems.
Dark Souls is this to the point of being a Kudzu Plot. There is very little in the way of story progressing Cutscene, and very little is directly explained to you. You can gain a bits of understanding about the setting, the past, and what is currently going on by compiling NPC dialogue, item Flavor Text, and by observing your surroundings.
The first Metroid Prime game does this to the largest degree. It is wholly possible to go through the entire game without even knowing what you're doing or why you're doing it. Scanning Chozo Lore and Pirate Logs as you find them will give you bite-sized pieces of information that can eventually be assembled to see the whole picture. Fortunately, the game introduces scanning early on and makes it a core element of gameplay, so it is much more difficult than it sounds to blunder cluesleslsly through everything. It definitely doesn't hurt that the game marks the story scans with the icon indicating that they are mission-critical. Echoes and Corruption have cutscenes that provide enough information for the player to know the general plot, though rich amounts of details and backstory still have to be scanned. Prime 2 requires to a degree that you scan luminoth bodies for the keybearer lore in order to beat the game.
Metroid Prime Hunters requires you to piece together the plot without the aid of cutscenes or expository sequences. And much of the information has to be taken from haphazardly-scattered, scannable data caches which are only visible to your scan visor. Yes, it is ludicrously easy to walk right by the entire story and not even realize it.
A Valley Without Wind is very open-ended, and set up in such a way players make the plot as they go along. It does this by dropping the player into the world without a single clue as to exactly what put it in this state to begin with. The player has to unlock various "mysteries", then seek out secret missions to earn precious scraps of backstory piece by piece.
Knights of the Old Republic II. If you listen accurately to what Kreia and other teammates tell you, play a Lightsider and learn everything you can from the Jedi Masters, and play the game several times that way, you might actually be able to figure out just what happened during the complicated backstory, which is also full of contradictions because several characters just flat-out lie.
Zombies, Run! indulges in this a fair bit. The first mission introduces someone firing on a helicopter with a missile launcher, which gets touched on now and then but never resolved. The relationship with New Canton comes in, gets dropped, and then comes back again. Bit by little bit, the dual storylines explaining how Abel Township is surviving and how the plague began get resolved.
Desktop Dungeons implements this, in part, to deal with the fact that there's no single linear path for the plot to take. Information about the backstory is often doled out in class challenges and boss monologues.
Higurashi: When They Cry constructs a typical jigsaw, with the added twist that in each route it offers false explanations for what's going on, only to debunk them in later arcs. Some are obviously bogus. Alien invasion!?
In fact, the final arc features a literal puzzle where you have to piece the TIPS (basically, hints and backstories) together.
Umineko: When They Cry, its sister series, does the same. Its constant retelling of the main story gives you, bit by bit, clues to solve the mystery. Unlike Higurashi, while the author gives just enough clues to figure out the solutions yourself, don't expect any answer to be given directly: even after the series has ended, a number of explanations remain largely Fanon. Not at all coincidentally, the main aesop of the series is to believe in your own truth without denying those of other people. Also, the manga adaptation gives numerous additional clues or clarifications (mostly in Episode 8).
Remember 11 has a pretty serious case of this. If you don't get any bad ends, it's a fairly coherent story with most of the unanswered questions being possible to figure out, if not easy. But the more bad ends you get, the more material you have to work with such as why everything is happening, who everyone is and everything else. When you have the most information about the story is when you truly realize you have no idea what just happened, and you never will know for sure.
Fate/stay night has three routes focusing on different enemies, with different plans that were barely referenced in the earlier ones.
Tsukihime even more so, with five routes, each focused on different aspects of the story.
Lux-Pain to the point that IGN gave it a low rating because they didn't understand the story. The game makes sense if you play at least two to three times (and a game like this only takes at least 24 hours to beat) and read between the lines and choose different dialogue choices as well as reading the information that the game gives you at the beginning concerning character information, place location, SILENT, and the overall mission that the game doesn't bother to explain in the first five minutes. That's all in the manual. Otherwise, this story makes perfect sense.
And if you can decipher the fog of bad translation IN A TEXT BASED GAME, and you don't write off the game due to the bad pacing and bad translation giving you a bad impression of the game.
The Ace Attorney games love this trope, especially the 'Phoenix Arc'. Each game has its own self contained story arc, as does each case, making you figure out the entire plot as the trials progress. The Phoenix Arc comprises three games, a total of 14 cases with a recurring cast of characters, with ALL the mysteries and past problems of Phoenix, Maya and Mia as well as a healthy does of Edgeworth's and Gumshoe's slowly being revealed, connected, explained and resolved.
Gunnerkrigg Court: A bizarre fantasy/science-fiction mixture with loads of unresolved mysteries. Fans sometimes joke that for every question a chapter answers, it brings up at least 10 more. Author Tom Sidell has a Word of God mail slot, but doesn't give away much. Coyote even lampshaded this in-story.
Goblins has something of a Jigsaw Puzzle Plot, with various Cryptic Prophecies and two current main story arcs, with a couple of other villains floating around, all of which seem likely to come into confluence at some point.
Last Res0rt not only has a Jigsaw Puzzle Plot, it actually LAMPSHADES this; the working title of the series was actually "Jigsaw's Puzzle" until the show became a bigger focus than the character.
Sluggy Freelance is either this or a straight up Kudzu Plot, depending on who you ask during what arc. It has got so thick on details that Pete's started including reference links to the archives, in case readers have forgotten the plot point he's currently explaining. At least a lot of the plots, especially earlier on, seem to get resolved by the end of a story; it may be (intentionally) impossible to tell what's really going on, but it's not too confusing to figure out what happens and is revealed during a particular plot before another story comes in and reveals that wasn't all.
Erfworld requires a huge amount of attention to detail just to figure out the rules of the world, and that still leaves the mystery of what exactly the world is, and who is working behind the scenes.
Bob and George. Started out as a filler sprite comic while the author learned how to draw, stuff kept happening and we end up with multiple parallel universes, various alternate timelines, clones, doppelgangers, etc. And it still all worked out in the end. David Anez is either the most talented jigsaw plotter ever or the King of Ass Pull. Possibly both.
El Goonish Shive, and thanks to Dan Shive's bitter refusal to ever tie things up, some of the pieces just collect dust.
Girl Genius has plot elements that are still being worked out and mysteries in the main plot that started on the third page.
Surprisingly, The Adventures of Dr. McNinja is showing signs of this, courtesy of King Radical, Charles Goodrich and Frans Rayner, in that order.
Homestuck - A video game turns out to be a harbinger of the apocalypse, destroying the world while the players, including one raised by a spacetime-bending dog, escape to timeless alternate universes to break stalemates between anthropomorphic chess pieces while aided by strange beings from a ruined world; meanwhile, aliens from another alternate universe have recently finished playing the same game by subtly different rules while tending to multiversal Eldritch Abominations. Then it just gets confusing...
This is Lampshaded; the term "Ultimate Riddle" is mentioned by a few characters. During one section the reader progresses through the story by clicking on pictures that fell from a scrapbook, which metaphorically translates into the reader picking up pieces that fell from a puzzle and seeing how they all fit.
According to Andrew Hussie himself, this trope is probably the best summary of Homestuck we're gonna get:
"The thing is, Homestuck is both a story and a puzzle, by design and by definition. If asked to define it, “a story that’s also a puzzle” is as close to true as any answer I’d give."
uu: I HAVE NOTICED. AS YOuR AWFuL MEANDERING SAGA WENDS ITS WAY. THROuGH THE ASS CRACK OF NOWHERE AND BACK.
uu: ANSWERS TO POINTLESS QuESTIONS ARE OFTEN DEFERRED. NIGH INDEFINITELY.
In Creative Release, figuring the actual plot out (versus the phenomena it provokes) is akin to a puzzle game. Most pages contain hints, but that's just what they are - hints. Connecting the various hints together is hardly easy.
The Mansion of E tends to spend more time leisurely exploring the eponymous structure more than answering plot questions.
"Ruby Nation" forms its story with scenes and textual ephemera from various points in the timeline, often revealing information out-of-sequence (such as with Elise's brainwashing).
The series lonelygirl15 is notably reticent to explain any more than about half of what's going on at any given time.
KateModern is a mild example, successfully building up and maintaining various mysteries.
Ruby Quest; by the end, you still don't have all the pieces. Apparently more could have been gotten if certain actions had been taken. Or more could have been missed, or course. Word of God answered quite a few things, though.
The Mechakara saga on Atop the Fourth Wall. Lewis has stated that every appearance of Mechakara contains some kind of clue to his identity or his ultimate goal against him.
Whateley Universe. It took years to find out what really happened to Cavalier and Skybolt, and now even some of the main characters are struggling to figure out who Hekate's Master really is. And that's after well over a hundred novels, novellas, and short stories.
And now Chaka has gotten a mystical prophecy no one in-story can figure out, so the puzzle pieces are getting waved in our faces.
There's a sci-fi game currently going on (as of late April 2011) called Vanished where we're supposedly getting contacted from the future. The world has supposedly undergone a huge environmental disaster and everybody's trying to figure out what's going on. Oh, and we've got about a few thousand teenagers helping and... we've got a lot of the puzzle pieces figured out.
Shadow Of Israphel is looking this way. We still have no idea who Israphel is, except that he's apparently Reverend_John's son, who's supposed to have been dead for 5 years, and yet has been haunting Old_Peculiar for much longer than that. Oh, and he has 2 graves. The greatest threat to the world is SAND. Except that the Sand is actually a prison for an army of giant evil robots What? And we still have no idea what the facilities in The Nether are, who N-Comm Systems are and how they are from the future, what the Sentinels actually are, what the Turtle God was, how Shiplord_Hubert ended up in The Desert, who the Templar Kings are, and a whole lot more.
Worm introduces several mysteries as part of the central plot that gradually unfold over the course of the story, most notably the nature of parahuman powers, the origins of the Endbringers, everything about Cauldron, and the impending apocalypse.
12 oz. Mouse is one of the crowning achievements in narrative complexity. Between the incredibly complicated plot and the...interesting animation, most people watch it without noticing that there's any plot at all. Seriously. Any discussion of the show immediately turns into "there's no point to it" versus "what the hell are you talking about?"
While the overall plot of The Venture Bros. is fairly straightforward, some character arcs are very subtle. For example, put together Hank always trying to imitate Brock, Rusty fawning over Dean on the twins' birthday, and Hank's general dominance over Dean physically and emotionally, and you have a metric truckload of daddy issues.
Similar to The Venture Brothers, Adventure Time is fairly straightforward for the most part. However at the same time there are many subtle storylines and hints of backstory hidden beneath the surface that can be found if you look hard enough. Reading into Word of God from the creators and rewatching old episodes after major plot twists will reveal all sorts of things for you to put together. If the reveal that Ooo is set After the End or Ice King's origin and his connection to Marceline surprise you, look back at some old episodes to see how facts like this have been dangled in front of you since the first season.