Jigsaw Puzzle Plot

"Tommy: You see, Trumpy? The pieces go together! Tom Servo: If only this movie were so lucky..."

- Mystery Science Theater 3000, Pod People

Lots of interesting things are going on in the series' Myth Arc: Mind Screws, wild conspiracies, 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 escaping failing to escape deathtraps.

Anime and Manga

 * Revolutionary Girl Utena may just be the Trope Codifier among anime.
 * 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.
 * If you ever decide to bypass the Mind Screw of Neon Genesis Evangelion and try to decipher the plot (possibly via The Other Wiki), you can see how it was going for this category. Take Our Word for It, there are a whole mess of things going on here.
 * 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 has the distinction of being a Jigsaw Puzzle Plot where we're given a couple of pieces across twenty episodes...then an entirely new puzzle made for two-year-olds in the last six.
 * 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.
 * Baccano is a perfect example of this. The entire series is in Anachronic Order, with almost every major plot point being shown in the first episode but without enough context to put them together. It even includes the above mentioned style of Wham! Episode.
 * And being the Spiritual Successor to Baccano, Durarara does this, too.
 * 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.
 * Fullmetal Alchemist, both the original manga and the 2003 anime version in their own respective ways.
 * FLCL. Given this was made by the same people who made Neon Genesis Evangelion AND was written by the same man who wrote Revolutionary Girl Utena and Star Driver, this isn't much of a surprise, but still...
 * GetBackers 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 can be seen in contextually-relevant background scenes in Season 1, specifically on Kinue Crossroad's desk.
 * Paranoia Agent seems designed to confuse, bewilder and annoy.
 * Makes sense, as it's basically the unfinished, leftover "scraps" of story ideas from an already crazy writer/director.
 * 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.
 * Both Last Exile and Last Exile Fam the Silver Wing
 * Twentieth Century Boys alternates between present day and the childhood of the central characters, revealing major plot points, Chekhov's guns and backstories along the way.
 * Anything by Naoki Urasawa. Monster regarding Johan and his plans, Pluto trying to figure out the reasoning behind the murders, and Billy Bat regarding the... we're not sure yet
 * Ghost in The Shell Stand Alone Complex tends to generally Info Dump on viewers, especially during the one-of Stand Alone episodes. During the Complex episodes, the layered intricacy of the plotting is paid off in spades.
 * 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.
 * Karano 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.
 * Chrono Crusade seems to attempt to do this.
 * 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 ) and some things are touched on so quickly it's easy to miss them (like being half-demon or ).
 * 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.
 * Serial Experiments Lain

Comic Books

 * Grant Morrison writes a lot of these. It's not always a bad thing, though, just seems to be his style.
 * One Hundred 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.

Fan Fiction

 * Aeon Natum Engel succeeds in creating a Jigsaw Puzzle Plot where its source material failed (and no, knowing what was going on in canon Eva won't help you that much). Warning: Putting too many pieces together may induce maniacal laughter and/or gibbering.
 * 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.

Film

 * Vantage Point
 * Primer
 * Pod People
 * Memento
 * Inception
 * The Saw movies.
 * 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.
 * Citizen Kane
 * 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 corperation, the government, and an anti-corperete terrorist who seems to know something about the monster are all tied together.

Literature

 * A Song of Ice and Fire. It's surprising how much one can learn about the backstory and the Myth Arc from reading between the lines and putting together minor details.
 * Or going to The Other Wiki and having it explained to you.
 * 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...or does it?
 * Harry Potter, to the point where half the final book is made up of scenes where some object briefly mentioned earlier in the series becomes extremely important. In essence, it's a book of Plot Coupons being cashed in.
 * 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 an 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.
 * His Dark Materials
 * A Series of Unfortunate Events could be said to be the second variety.
 * 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 Cyber Punk 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.
 * Chronicle Of A Death Foretold

Live-Action TV

 * Twin Peaks. However, it was made up as the creators went along, 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. Your Mileage May Vary as to how well the overall plot was resolved.
 * Heroes put together an expertly crafted Jigsaw Puzzle Plot in Season 1, with almost all the loose threads neatly tied up. Subsequent seasons devolved into Random Events Plots (with the possible exception of Season 4 Redemption).
 * Arguably what 24 is all about. Things tend to get properly put together halfway through, though.
 * Babylon 5, pre-planned 5 year plot which was shifted by three episodes near the end due to the network threatening to cancel them a year short of the original ending, and where actors leaving and arriving meant that some functions were shifted to other characters while still getting the same effect.
 * The new Battlestar Galactica Reimagined. Like Lost above, they only began to plan out everything towards the end of season 1.
 * Unfortunately, it began suffering from The Chris Carter Effect after Season 2, and by the Grand Finale it was pretty clear that the writers were making it up as they went along.
 * The Prisoner arguably originated the trope for entire series.
 * The Twilight Zone (but within a single episode, rather than scattered across a Story Arc)
 * 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 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
 * 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.
 * House often has these - a tiny thing mentioned by the patient (or a patient's relative/acquaintance or Wilson) in the beginning will be the key to solving the mysterious illness that the patient is suffering from.
 * The Shadow Line does this, as it has many seemingly disparate plot points that only fall clearly into place in the final two episodes.

Video Games

 * Xenogears and Xenosaga are examples of this (probably the biggest ones in the entire RPG genre, if not the entire video game medium), with a little bit of Xanatos Roulette thrown in for good measure.
 * Xenoblade carries on the legacy, of course.
 * 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".
 * The Metal Gear Solid series is notorious for this. The plot of Metal Gear Solid 4 Guns of the Patriots basically consists of putting all the puzzle pieces together.
 * 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 Xanatos upon Xanatos, 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.
 * Killer 7 sets the puzzle pieces in front of you, takes a handful away, and leaves you to assemble the rest.
 * That's actually not far off, since Capcom forced Suda 51 to remove an entire half of the game that was supposed to cover the loose ends. It now only exists in the Hand in Killer7 book as the "Jacob Checkbox" reports.
 * Which actually contradict the game at several points. To continue the metaphor, it's like being handed the pieces to another puzzle instead of the one you're making.
 * 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.
 * Odin Sphere. The story prior to 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 Killer 7 example above, Suda 51's The Silver Case series follows this trope. It begins with Moonlight Syndrome, in which, 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. 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.
 * While Deus Ex's main story is pretty straight, the backstory is hidden in pieces in various in-game media this way.
 * Final Fantasy VIII aimed for subtle exposition, and never outright states its most important plot points (such as or the motivation of Big Bad ). Unfortunately, this became one of the biggest criticisms of the game as fans complained loudly about plot twists supposedly coming out of "nowhere" and others going unexplained.
 * 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.
 * 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.
 * 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.
 * The old and vast genre of adventure games (point-and-click, text, and the less antiquated first-person variety), where this trope was practically the whole point.
 * 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.
 * Bioshock has a fairly straightforward main plot. The settings backstory, on the other hand, is revealed mostly through audio recordings left behind by people who used to live in Rapture.
 * Blaz Blue: 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 unknowingly implies that she was that mercenary.
 * Hotel Dusk: Room 215 for the DS 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.
 * Nie R, 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.

Visual Novels

 * Higurashi no Naku Koro ni 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. !?
 * In fact, the final arc features a literal puzzle where you have to piece the TIPS (basically, hints and backstories) together.
 * Umineko no Naku Koro ni, it sequel, does the same. It constant retelling of the main story gives you, bit by bit, clues to solve the mystery.
 * 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 is comprised of 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.

Web Comics
""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.""
 * 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. The last year or so has been 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.
 * 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 Rainer, 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:

"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."
 * Lampshaded by uu as representative of the anti-fans of Homestuck:

Web Original

 * The series Lonelygirl15 is notably reticent to explain any more than about half of what's going on at any given time.
 * Kate Modern 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.
 * Marble Hornets, to the point of Mind Screw.
 * 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.

Western Animation

 * 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 Brothers 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.