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* ''Manga/PandoraHearts'': From beginning to end, there are hints that paint a bigger picture to the past and the backstories of each character,especially regarding the Tragedy of Sablier, Pandora, Abyss, Will of Abyss, and almost everything, really.And the mystery keeps you at the end of your seat. Not to mention the Alice In Wonderland themes and references that are already confusing and weird by themselves.
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* ''Manga/PandoraHearts'': From beginning to end, there are hints that paint a bigger picture to the past and the backstories of each character,especially regarding the Tragedy of Sablier, Pandora, Abyss, Will of Abyss, and almost everything, really. And the mystery keeps you at the end of your seat. Not to mention the Alice In Wonderland themes and references that are already confusing and weird by themselves.
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* ''Manga/ZeroSevenGhost'': The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems.Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
to:
* ''Manga/ZeroSevenGhost'': The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems. Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
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* ''LightNovel/{{Baccano}}'' is a perfect example of this. The entire series is in AnachronicOrder, with almost every major plot point being shown in the first episode but without enough context to put them together. It even includes the [[TheReveal above mentioned style]] of WhamEpisode. And being the SpiritualSuccessor, ''LightNovel/{{Durarara}}'' does this, too.
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* ''LightNovel/{{Baccano}}'' ''Literature/{{Baccano}}'' is a perfect example of this. The entire series is in AnachronicOrder, with almost every major plot point being shown in the first episode but without enough context to put them together. It even includes the [[TheReveal above mentioned style]] of WhamEpisode. And being the SpiritualSuccessor, ''LightNovel/{{Durarara}}'' ''Literature/{{Durarara}}'' does this, too.
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* ''LightNovel/TheGardenOfSinners'' due to the first four of its seven parts being in AnachronicOrder. Those unfamiliar with ''VisualNovel/{{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.
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* ''LightNovel/TheGardenOfSinners'' ''Literature/TheGardenOfSinners'' due to the first four of its seven parts being in AnachronicOrder. Those unfamiliar with ''VisualNovel/{{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.
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* ''LightNovel/RebuildWorld'': What are the MysteriousBacker VirtualSidekick Alpha's goals and motives, and that of her ArchNemesis Yanigisawa? The answer to that question is given in crumbs and hints over hundreds of chapters of the WebSerialNovel, often more than a dozen chapters going without it being furthered. The situation is complicated, so we get an occasional WhiteVoidRoom SharedDream between Akira and Alpha where she talks to others, or a scene from Yanigisawa, both of which sometimes contain TheReveal.
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* ''LightNovel/RebuildWorld'': ''Literature/RebuildWorld'': What are the MysteriousBacker VirtualSidekick Alpha's goals and motives, and that of her ArchNemesis Yanigisawa? The answer to that question is given in crumbs and hints over hundreds of chapters of the WebSerialNovel, often more than a dozen chapters going without it being furthered. The situation is complicated, so we get an occasional WhiteVoidRoom SharedDream between Akira and Alpha where she talks to others, or a scene from Yanigisawa, both of which sometimes contain TheReveal.
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* ''Manga/FullmetalAlchemist'', both the original manga and [[Anime/FullmetalAlchemist the 2003 anime version]] in their own respective ways.
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* ''Manga/FullmetalAlchemist'', both the original manga and [[Anime/FullmetalAlchemist the 2003 anime version]] ''Anime/FullmetalAlchemist2003'' in their own respective ways.
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* If you ever decide to bypass the MindScrew of ''Anime/NeonGenesisEvangelion'' and try to decipher the plot (possibly via [[Wiki/{{Wikipedia}} The Other Wiki]]), you can see how it was going for this category. TakeOurWordForIt, there ''are'' a whole mess of things going on here.
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* If you ever decide to bypass the MindScrew of ''Anime/NeonGenesisEvangelion'' and try to decipher the plot (possibly via [[Wiki/{{Wikipedia}} [[Website/{{Wikipedia}} The Other Wiki]]), you can see how it was going for this category. TakeOurWordForIt, there ''are'' a whole mess of things going on here.
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* ''Manga/SaintSeiyaEpisodeGA'': The story is actually at what will be the seventh published volume, yet there is still no clear plot.
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* ''Manga/SaintSeiyaEpisodeGA'': ''Manga/SaintSeiyaEpisodeGAssassin'': The story is actually at what will be the seventh published volume, yet there is still no clear plot.
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* ''Anime/{{FLCL}}''. Given this was made by the [[Creator/StudioGainax same people]] who made ''Anime/NeonGenesisEvangelion'' AND was written by the same man who wrote ''Anime/RevolutionaryGirlUtena'' and ''Anime/StarDriver'', this isn't much of a surprise, but still... Note that this show is only 6 episodes long and ''very'' fast-paced, meaning it's not hard to lose track of most of your pieces if you aren't paying attention.
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* ''Anime/{{FLCL}}''. Given this While ''Anime/{{FLCL}}'' is upfront with its ComingOfAgeStory and MonsterOfTheWeek aspects, the MythArc the latter is based on ([[spoiler:including that the co-protagonist was made by half of the [[Creator/StudioGainax same people]] who made ''Anime/NeonGenesisEvangelion'' AND was written by the same man who wrote ''Anime/RevolutionaryGirlUtena'' and ''Anime/StarDriver'', this isn't BigBadEnsemble]]) is much of a surprise, but still... Note that this show is more opaque--the protagonist himself only 6 episodes long and ''very'' fast-paced, meaning it's not hard to lose track of most of your pieces if you aren't paying attention.passively interacts with it at all.
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* ''Manga/ZeroSevenGhost'':The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems.Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
to:
* ''Manga/ZeroSevenGhost'':The ''Manga/ZeroSevenGhost'': The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems.Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
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* ''LightNovel/RebuildWorld'': What are the MysteriousBacker VirtualSidekick Alpha's goals and motives, and that of her ArchNemesis Yanigisawa? The answer to that question is given in crumbs and hints over hundreds of chapters of the WebSerialNovel, often more than a dozen chapters going without it being furthered. The situation is complicated, so we get an occasional WhiteVoidRoom SharedDream between Akira and Alpha where she talks to others, or a scene from Yanigisawa, both of which sometimes contain TheReveal.
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* ''Manga/{{Amatsuki}}'', particularly concerning the backstory and the real world timeline.
* ''Manga/AttackOnTitan'' throws several curveballs regarding the nature and motives of Titans within the series, most of which just raise more questions than provide answers.
** Every time there's a [[TheReveal reveal]], nothing is ever ''actually'' answered because we're provided with so much new information that all previous knowledge about a character or a concept is rendered useless. Most notably occurs after [[spoiler:the characters finally get to Eren's basement and learn the truth about the world. Well, kind of]]. All the [[UnreliableNarrator Unreliable Narrators]] don't help either, and nobody in-universe really knows what's going on themselves.
* ''LightNovel/{{Baccano}}'' is a perfect example of this. The entire series is in AnachronicOrder, with almost every major plot point being shown in the first episode but without enough context to put them together. It even includes the [[TheReveal above mentioned style]] of WhamEpisode. And being the SpiritualSuccessor, ''LightNovel/{{Durarara}}'' does this, too.
* ''Anime/TheBigO'' 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 ExecutiveMeddling are false; the "original" ending to the second and last season was only slightly more coherent).
* ''Manga/ChronoCrusade'' 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 [[spoiler:the demons being aliens]]) and some things are touched on so quickly it's easy to miss them (like [[spoiler:Satella and Fiore]] being half-demon or [[spoiler:Joshua and Azmaria being married in the epilogue]]).
** The anime version reveals things a little more smoothly, but thanks to its GeckoEnding 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.
* ''Anime/EdenOfTheEast''. 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.
* ''Anime/{{FLCL}}''. Given this was made by the [[Creator/StudioGainax same people]] who made ''Anime/NeonGenesisEvangelion'' AND was written by the same man who wrote ''Anime/RevolutionaryGirlUtena'' and ''Anime/StarDriver'', this isn't much of a surprise, but still... Note that this show is only 6 episodes long and ''very'' fast-paced, meaning it's not hard to lose track of most of your pieces if you aren't paying attention.
* ''Manga/FullmetalAlchemist'', both the original manga and [[Anime/FullmetalAlchemist the 2003 anime version]] in their own respective ways.
* ''Manga/FutureDiary'' has several important plot points that aren't fully explained until near the end. Something is clearly wrong with Yuno (even aside from all the [[{{Yandere}} other]] [[AxCrazy things]]), and then there's Murmur, who seems to have [[DragonWithAnAgenda her own plans]] for the Survival Game. [[AmateurSleuth Aru Akise]] is attempting to investigate the mysteries surrounding Yuno, but he doesn't have much success until near the end of the story.
* ''LightNovel/TheGardenOfSinners'' due to the first four of its seven parts being in AnachronicOrder. Those unfamiliar with ''VisualNovel/{{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.
* ''Manga/{{Gantz}}'''s only excuse for a MrExposition is a SnarkKnight UnreliableExpositor, and the protagonists' only other way of figuring out the rules by which their world operates is trial and error. As for ''why'' they're brought back from the dead, given all kinds of high-tech weaponry, and sent out to fight what are apparently aliens that [[TheMasquerade no one else can see]]? The hints are portioned out very slowly over [[LongRunner dozens of manga volumes]], and any or all of them may be {{Red Herring}}s. {{Lampshaded}} when an IntrepidReporter is taken on a tour of a factory that apparently manufactures the Gantz balls and weaponry by a friendly German gentleman who spins a tale of an IdiotSavant child under extraterrestrial influence inventing the tech... and then turns into an alien, mocks him for believing any of it, and disappears.
* ''Anime/{{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.
* ''Manga/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.
* ''Anime/GhostInTheShellStandAloneComplex'' tends to generally {{Infodump}} on viewers, especially during the one-of [[{{Filler}} Stand Alone]] episodes. During the [[MythArc Complex]] episodes, the layered intricacy of the plotting is paid off in spades.
* ''Manga/{{Kekkaishi}}'' and all the stuff relating to Karasumori and the Urakai.
* ''Anime/MobileSuitGundam00'': One example suffices; the primary design for [[spoiler: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.
* If you ever decide to bypass the MindScrew of ''Anime/NeonGenesisEvangelion'' and try to decipher the plot (possibly via [[Wiki/{{Wikipedia}} The Other Wiki]]), you can see how it was going for this category. TakeOurWordForIt, there ''are'' a whole mess of things going on here.
** Due to artistic reasons or whatnot, it's almost impossible to piece together some of the puzzles in the Series on its own, therefore REQUIRING third party material to be explained. Annoyingly enough, the Third Party Material itself often adds MORE questions which are not resolved.
*** A specific example [[InUniverse within the series]] neatly and unexpectedly shows during [[UnresolvedSexualTension Shinji and Asuka's first and]] ''[[UnresolvedSexualTension only]]'' [[UnresolvedSexualTension kiss]] near the end of Episode 15. The scene is strange and memorable. After it, Shinji and Asuka handle each other far more coldly. The series does not explain this repulsion until Episode 22, during a visual breakdown of Asuka's intents and personality.
* ''Anime/{{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.
* ''Manga/OnePiece'', 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.
* ''Manga/PandoraHearts'': From beginning to end, there are hints that paint a bigger picture to the past and the backstories of each character,especially regarding the Tragedy of Sablier, Pandora, Abyss, Will of Abyss, and almost everything, really.And the mystery keeps you at the end of your seat. Not to mention the Alice In Wonderland themes and references that are already confusing and weird by themselves.
* ''Anime/ParanoiaAgent'' seems designed to confuse, bewilder and annoy. It's basically the unfinished, leftover "scraps" of story ideas from [[Creator/SatoshiKon an already crazy writer/director]].
* ''Anime/{{Penguindrum}}''. It makes little sense till the last two episodes.
* ''Anime/PrincessTutu''. 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.
* ''Anime/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 ''[[TheStinger 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.
* ''Anime/RedGarden'' 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.
* ''Anime/RevolutionaryGirlUtena'' may just be the TropeCodifier among anime. ''Anime/StarDriver'', from the same writer, also fits ''very'' well.
* ''Manga/SaintSeiyaEpisodeGA'': The story is actually at what will be the seventh published volume, yet there is still no clear plot.
* ''Anime/SerialExperimentsLain'' has this since the plot is one big MindScrew.
* ''Anime/{{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.
* The anime version of ''Manga/{{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.
* ''Manga/TsubasaReservoirChronicle'' it seems straightforward up until the revelation about the clones and time travel.
* Anything by Creator/NaokiUrasawa. ''Manga/TwentiethCenturyBoys'' alternates between present day and the childhood of the central characters, revealing major plot points, [[ChekhovsGun Chekhov's guns]] and backstories along the way. ''Manga/{{Monster}}'' regarding Johan and his plans, ''Manga/{{Pluto}}'' trying to figure out the reasoning behind the murders, and ''Manga/BillyBat'' regarding the… [[MindScrew it's not quite clear]].
* Much like ''Anime/RahXephon'', ''Anime/WolfsRain'' 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.
* ''Anime/YuGiOhArcV'''s plot about the Dark Duelist (who for some reason looks just like [[TheProtagonist Yuya]]) Yuto and his home, and how he connects to Yuzu. In-between [[TheHero Yuya]]-centered episodes, we'll get episodes dedicated to Yuzu's interactions with him. Each interaction unveils something to the layer of complexity, and goes more into explaining Yuto's story: he comes from a now-destroyed world [[Anime/YuGiOhZexal that may be Heartland City]], has an enemy in form of [[Anime/YuGiOh5Ds a Synchro-using D-Wheeler]] named Yugo, a mysterious GreaterScopeVillain in the form of [[Anime/YuGiOhGX Academia]], and [[spoiler: a possible counterpart of Yuzu]] named Ruri. What's stopping us (and Yuzu, much to her annoyance) from getting everything right away is that Yuto is forcibly teleported away by Yuzu's bracelet whenever Yuya shows up. [[spoiler:We finally get answers about Yuto when he personally meets Yuya. And reveals everything about himself. We are thrown more into a loop when the secrets of Yuya, Yuto, and Yuzu just get more confusing with the reveal that there's one counterpart for Yuya and Yuzu in all four of the dimensions. All the counterparts appear to have magical powers, Yuya and his counterparts appear to have a magical BerserkMode that's somehow connected to their dragon-based monsters, and Yuzu and her counterparts are being hunted down by the BigBad.]]
** The second arc becomes even more complex, with the protagonists traveling to another world [[spoiler: that turns out to be an AlternateUniverse version of Anime/YuGiOh5Ds]] and suddenly the story starts focusing on the class war and brutal dystopia of this world, while at the same time keeping the previous plot about inter-dimensional wars still relevant. Unfortunately, there are two separate factions in this worlds government who have different as of yet unknown agendas for the protagonists, neither of which can be trusted, one outright antagonistic towards them and possibly working with Academia, plus a potential rebellion rising up amongst the lower class due to economic and societal issues apparently unrelated to the war. ''And'' we still don't know what [[TheChessmaster Reiji's]] full plan is.
** In the end, some seemingly separate mysteries were answered together, so as to unite every smaller mystery into the overall plot. (Ex, the mystery of why Yusho vanished three years ago also explains [[spoiler: what secrets Reiji Akaba was keeping and what his main goal is.]])
* ''Manga/ZeroSevenGhost'':The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems.Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
----
* ''Manga/AttackOnTitan'' throws several curveballs regarding the nature and motives of Titans within the series, most of which just raise more questions than provide answers.
** Every time there's a [[TheReveal reveal]], nothing is ever ''actually'' answered because we're provided with so much new information that all previous knowledge about a character or a concept is rendered useless. Most notably occurs after [[spoiler:the characters finally get to Eren's basement and learn the truth about the world. Well, kind of]]. All the [[UnreliableNarrator Unreliable Narrators]] don't help either, and nobody in-universe really knows what's going on themselves.
* ''LightNovel/{{Baccano}}'' is a perfect example of this. The entire series is in AnachronicOrder, with almost every major plot point being shown in the first episode but without enough context to put them together. It even includes the [[TheReveal above mentioned style]] of WhamEpisode. And being the SpiritualSuccessor, ''LightNovel/{{Durarara}}'' does this, too.
* ''Anime/TheBigO'' 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 ExecutiveMeddling are false; the "original" ending to the second and last season was only slightly more coherent).
* ''Manga/ChronoCrusade'' 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 [[spoiler:the demons being aliens]]) and some things are touched on so quickly it's easy to miss them (like [[spoiler:Satella and Fiore]] being half-demon or [[spoiler:Joshua and Azmaria being married in the epilogue]]).
** The anime version reveals things a little more smoothly, but thanks to its GeckoEnding 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.
* ''Anime/EdenOfTheEast''. 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.
* ''Anime/{{FLCL}}''. Given this was made by the [[Creator/StudioGainax same people]] who made ''Anime/NeonGenesisEvangelion'' AND was written by the same man who wrote ''Anime/RevolutionaryGirlUtena'' and ''Anime/StarDriver'', this isn't much of a surprise, but still... Note that this show is only 6 episodes long and ''very'' fast-paced, meaning it's not hard to lose track of most of your pieces if you aren't paying attention.
* ''Manga/FullmetalAlchemist'', both the original manga and [[Anime/FullmetalAlchemist the 2003 anime version]] in their own respective ways.
* ''Manga/FutureDiary'' has several important plot points that aren't fully explained until near the end. Something is clearly wrong with Yuno (even aside from all the [[{{Yandere}} other]] [[AxCrazy things]]), and then there's Murmur, who seems to have [[DragonWithAnAgenda her own plans]] for the Survival Game. [[AmateurSleuth Aru Akise]] is attempting to investigate the mysteries surrounding Yuno, but he doesn't have much success until near the end of the story.
* ''LightNovel/TheGardenOfSinners'' due to the first four of its seven parts being in AnachronicOrder. Those unfamiliar with ''VisualNovel/{{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.
* ''Manga/{{Gantz}}'''s only excuse for a MrExposition is a SnarkKnight UnreliableExpositor, and the protagonists' only other way of figuring out the rules by which their world operates is trial and error. As for ''why'' they're brought back from the dead, given all kinds of high-tech weaponry, and sent out to fight what are apparently aliens that [[TheMasquerade no one else can see]]? The hints are portioned out very slowly over [[LongRunner dozens of manga volumes]], and any or all of them may be {{Red Herring}}s. {{Lampshaded}} when an IntrepidReporter is taken on a tour of a factory that apparently manufactures the Gantz balls and weaponry by a friendly German gentleman who spins a tale of an IdiotSavant child under extraterrestrial influence inventing the tech... and then turns into an alien, mocks him for believing any of it, and disappears.
* ''Anime/{{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.
* ''Manga/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.
* ''Anime/GhostInTheShellStandAloneComplex'' tends to generally {{Infodump}} on viewers, especially during the one-of [[{{Filler}} Stand Alone]] episodes. During the [[MythArc Complex]] episodes, the layered intricacy of the plotting is paid off in spades.
* ''Manga/{{Kekkaishi}}'' and all the stuff relating to Karasumori and the Urakai.
* ''Anime/MobileSuitGundam00'': One example suffices; the primary design for [[spoiler: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.
* If you ever decide to bypass the MindScrew of ''Anime/NeonGenesisEvangelion'' and try to decipher the plot (possibly via [[Wiki/{{Wikipedia}} The Other Wiki]]), you can see how it was going for this category. TakeOurWordForIt, there ''are'' a whole mess of things going on here.
** Due to artistic reasons or whatnot, it's almost impossible to piece together some of the puzzles in the Series on its own, therefore REQUIRING third party material to be explained. Annoyingly enough, the Third Party Material itself often adds MORE questions which are not resolved.
*** A specific example [[InUniverse within the series]] neatly and unexpectedly shows during [[UnresolvedSexualTension Shinji and Asuka's first and]] ''[[UnresolvedSexualTension only]]'' [[UnresolvedSexualTension kiss]] near the end of Episode 15. The scene is strange and memorable. After it, Shinji and Asuka handle each other far more coldly. The series does not explain this repulsion until Episode 22, during a visual breakdown of Asuka's intents and personality.
* ''Anime/{{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.
* ''Manga/OnePiece'', 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.
* ''Manga/PandoraHearts'': From beginning to end, there are hints that paint a bigger picture to the past and the backstories of each character,especially regarding the Tragedy of Sablier, Pandora, Abyss, Will of Abyss, and almost everything, really.And the mystery keeps you at the end of your seat. Not to mention the Alice In Wonderland themes and references that are already confusing and weird by themselves.
* ''Anime/ParanoiaAgent'' seems designed to confuse, bewilder and annoy. It's basically the unfinished, leftover "scraps" of story ideas from [[Creator/SatoshiKon an already crazy writer/director]].
* ''Anime/{{Penguindrum}}''. It makes little sense till the last two episodes.
* ''Anime/PrincessTutu''. 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.
* ''Anime/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 ''[[TheStinger 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.
* ''Anime/RedGarden'' 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.
* ''Anime/RevolutionaryGirlUtena'' may just be the TropeCodifier among anime. ''Anime/StarDriver'', from the same writer, also fits ''very'' well.
* ''Manga/SaintSeiyaEpisodeGA'': The story is actually at what will be the seventh published volume, yet there is still no clear plot.
* ''Anime/SerialExperimentsLain'' has this since the plot is one big MindScrew.
* ''Anime/{{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.
* The anime version of ''Manga/{{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.
* ''Manga/TsubasaReservoirChronicle'' it seems straightforward up until the revelation about the clones and time travel.
* Anything by Creator/NaokiUrasawa. ''Manga/TwentiethCenturyBoys'' alternates between present day and the childhood of the central characters, revealing major plot points, [[ChekhovsGun Chekhov's guns]] and backstories along the way. ''Manga/{{Monster}}'' regarding Johan and his plans, ''Manga/{{Pluto}}'' trying to figure out the reasoning behind the murders, and ''Manga/BillyBat'' regarding the… [[MindScrew it's not quite clear]].
* Much like ''Anime/RahXephon'', ''Anime/WolfsRain'' 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.
* ''Anime/YuGiOhArcV'''s plot about the Dark Duelist (who for some reason looks just like [[TheProtagonist Yuya]]) Yuto and his home, and how he connects to Yuzu. In-between [[TheHero Yuya]]-centered episodes, we'll get episodes dedicated to Yuzu's interactions with him. Each interaction unveils something to the layer of complexity, and goes more into explaining Yuto's story: he comes from a now-destroyed world [[Anime/YuGiOhZexal that may be Heartland City]], has an enemy in form of [[Anime/YuGiOh5Ds a Synchro-using D-Wheeler]] named Yugo, a mysterious GreaterScopeVillain in the form of [[Anime/YuGiOhGX Academia]], and [[spoiler: a possible counterpart of Yuzu]] named Ruri. What's stopping us (and Yuzu, much to her annoyance) from getting everything right away is that Yuto is forcibly teleported away by Yuzu's bracelet whenever Yuya shows up. [[spoiler:We finally get answers about Yuto when he personally meets Yuya. And reveals everything about himself. We are thrown more into a loop when the secrets of Yuya, Yuto, and Yuzu just get more confusing with the reveal that there's one counterpart for Yuya and Yuzu in all four of the dimensions. All the counterparts appear to have magical powers, Yuya and his counterparts appear to have a magical BerserkMode that's somehow connected to their dragon-based monsters, and Yuzu and her counterparts are being hunted down by the BigBad.]]
** The second arc becomes even more complex, with the protagonists traveling to another world [[spoiler: that turns out to be an AlternateUniverse version of Anime/YuGiOh5Ds]] and suddenly the story starts focusing on the class war and brutal dystopia of this world, while at the same time keeping the previous plot about inter-dimensional wars still relevant. Unfortunately, there are two separate factions in this worlds government who have different as of yet unknown agendas for the protagonists, neither of which can be trusted, one outright antagonistic towards them and possibly working with Academia, plus a potential rebellion rising up amongst the lower class due to economic and societal issues apparently unrelated to the war. ''And'' we still don't know what [[TheChessmaster Reiji's]] full plan is.
** In the end, some seemingly separate mysteries were answered together, so as to unite every smaller mystery into the overall plot. (Ex, the mystery of why Yusho vanished three years ago also explains [[spoiler: what secrets Reiji Akaba was keeping and what his main goal is.]])
* ''Manga/ZeroSevenGhost'':The mysteries present themselves throughout the story and are resolved but even those resolutions have many layers and nothing is what it seems.Both with the characters and the 7 Ghosts. The basic storyline itself hides so many twists and turns, especially when you look back to earlier interactions and events.
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