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  • Big-Lipped Alligator Moment: The third windmill video. The game already contains many audio logs and other videos with philosophical and spiritual quotes and teachings, but this video goes one step further. It's a 12-minute-long video of a man holding a candle. This clip is the end of the 1983 movie Nostalghia by Andrei Tarkovsky, known for his dry, difficult style and highly metaphysical themes. The scene already qualifies as a Gainax Ending even taken on the context of the whole movie. Now, imagine watching the scene without said context, and you'll end the video asking yourself "What have I just watched?"
  • Broken Base:
    • The $40 USD price was a point of contention, as it rivaled some console games and made The Witness one of the most expensive indie video games of all time, if not the most. The core argument was whether the quality of the game justified the price or not. Seven years of development went into the game, and it includes a wide variety of content. There's also the licensing of video content, including from the BBC. However, the style of gameplay has its own stigma around it, as the game is largely a vehicle for puzzles with little effort made to include traditional "rewards" for solving them. As a result, Jonathan Blow commented that it became the most popular torrent at the time of its release, which would delay his ability to make a third game. In a curious bit of irony, the game was made available for free download on the PS4 in 2021.
    • Blow also mentioning that his next game would potentially have DRM in an effort to prevent the above from happening again caused a lot of heated discussion.
    • This video by Joseph Anderson describes how some players felt conflicted about the game.
  • Epileptic Trees: Thanks to the inclusion of a meta puzzle or two (as well as some cleverly hidden perspective artwork), fans have deeply analyzed every single thing in the game to see if there are any additional puzzles or super-secret hidden purpose behind it.
  • Fridge Brilliance: The meaning behind the symbols used to represent some puzzle mechanics. The "Tetris" blocks are directly interpretable as a figure, as is the "star" symbol (in treehouses), which is the superposition of two squares (and thus means "double"). The "annulation" symbol can be interpreted as an antibody, which makes quite a bit of sense: antibodies are produced to neutralize harmful bacteria and viruses, or in this case an unsatisfied puzzle symbol.
  • Good Bad Bugs:
    • Early versions of the game contained strange glitches where completing specific puzzles under specific conditions would lead to completely unexpected results:
      • In the red portion of the swamp (the last portion before activating the laser), solving the puzzle that lowers the yellow cubes in a specific way makes disappear a large purple cube in a completely unrelated zone of the swamp, even though the purple cube serves only to decorative purposes.
      • Early in the game, you can find a locked vault with a puzzle involving hexagonal dots and black and white squares. Much later, in the quarry, you can find a puzzle which is completely identical to the aforementioned puzzle except that it adds an annulation symbol. It's been reported that in earlier versions, solving the latter puzzle would open the vault even if the former puzzle hadn't been solved yet. However, this is an extremely rare situation, since it's unlikely the vault puzzle hasn't been solved by the time the player is able to reach said quarry puzzle.
    • In a more recent version, it's apparently possible to steer the boat into the island by stopping it at a dock while it's at full speed.
    • There are two known exploits that can make The Challenge much easier to complete:
      • On the PS4 port there was a sort of loophole which allowed the player to pause the game without resetting The Challenge. This was done by putting the console in rest mode, which suspends the game state and does not count as a pause. This was later patched in an update, mostly to the dismay of trophy hunters. Through patch reversion it is still possible to take advantage of this loophole, however, the player will need to restart from a fresh save file, as loading up a save file from a newer version while playing on an older version of the game will crash the game.
      • A lesser-known exploit on PS4 (which was never patched) disables the timer on The Challenge for the last (and hardest) set of puzzles, after the song ends. To trigger this glitch, the player needs to wait for the song to end and then count to three before completing the second maze triangle puzzle. The timing is a bit tricky, so a few attempts might be needed to trigger the glitch. Here is a video for reference.
  • Memetic Mutation: Jonathan Blow's piss jar.Explanation 
  • Narm:
    • The secret ending is described on YouTube as watching either someone who's either drunk, on drugs, or filming a HowToBasic video.
    • The game's quotations easily get ridiculous, but one that stands out in particular is a quote in the mountain about koans, which implicitly compares the game's puzzles to them. It talks about how koans can be contemplated in an attempt to create a logic bomb that creates a moment of unmediated experience with the world, in a room with puzzles that have logical solutions, and thus are not liable to create logic bombs. Even if the koans are just a foil for the puzzles, it's an absolutely ridiculous comparison whose starting point – going off of a quote in the autumnal forest – seems to be just that the puzzles' concepts are not taught to the player with language.
  • Paranoia Fuel: In the Hall of the Mountain King, which plays during the mountain puzzles is one of the most anxiety-inducing pieces of Classical Music you will ever hear.
  • Scrappy Mechanic:
    • The self-disabling panels. Many panels in the game are connected via wires that indicate the power flowing from one to another. A lot of these panels disable themselves when a wrong solution is entered, forcing you to return to the previous panel and reenter the correct solution to turn on the next panel again. Theoretically, this serves to discourage the player from brute forcing puzzles, but there are several problems with this. The first problem is the nebulous criteria that the game chooses to determine which puzzles self-disable.Explanation  The second problem is the bad job this mechanic does at what's intended. Explanation  The final problem is the question of whether it's even worth to try to prevent the player from brute forcing a puzzle. Explanation 
    • Believe it or not, the saving mechanic can be considered this. The game, while allowing you to save and quit at any point, does not have any dedicated save slots, and only has auto-save files. What this basically means is if you decide to start a new game, you run the risk of losing your "completed" save file if you don't load it back up every now and then to keep it on the top of the list.
  • Spiritual Successor: Very much in the style of Myst (even more so its sequel Riven), with the lonely Beautiful Void and numerous puzzles aimed towards a common goal. It even contains a swampy treehouse area!
  • That One Level:
    • The desert puzzles revolve around reflection of light on the panels to reveal the correct paths drawn on them. The basement of the desert temple contains puzzles based on water reflection — the principle is the same, but this time you have to arrange the water level of a pool below the panels to reflect at the right angles to see the solutions. While this puzzle is hard enough since the water reflects the solutions upside-down, the really annoying thing is that the water cannot be paused between its highest and lowest points; if you don't get the solution, you'll have to wait for the pool level to rise or lower completely before you can try again. This is especially bad because the speed at which the water level changes is super slow.
    • The jungle, and not only because of its associated mechanic (already covered under That One Puzzle). It has the hardest to find starting puzzle of any section (and the most confusing area layout overall). There is a section of sound puzzles where there are intentionally confusing sounds, including really annoying ones like a telephone ringing (even the bird chirps themselves are much more annoying than a pleasant musical tone would have been). The second section requires taking a detour to raise a wall with more puzzles, then taking another long detour to reach said puzzles. The final area of the jungle is a weird shepherd tone maze which serves no purpose other than confusing the player (even the laser box itself is the hardest one to find in the game, the only place you can see it from is the mountain top). And finally, the jungle is the only area of the game with an anti-shortcut! Everywhere else in the game has shortcuts that open up when you solve certain puzzles, but the jungle has a permanent pop-up wall instead, leaving one lovely path untraversable (and another one plagued with annoying noises) for the rest of the game.
    • The Challenge, the Brutal Bonus Level to end all puzzle game Brutal Bonus Levels. In a nutshell, it's a series of around a dozen or so randomized panels that all have to be solved within a very tight time limit (this in a game that, up until now, has been very much about taking your time to figure things out). This includes a set of three panels in which two panels are deliberately unsolvable, leaving you to waste time figuring out which one can be solved and then actually solving it. And it does this twice. And if you run out of time towards the end, it's a loooooong trek back to the record player to start over. And your reward for completing this madness? The line pattern for the final video... which then turns out to be part of an hour-long environmental puzzle. And you thought the cloud in Braid was bad....
  • That One Puzzle:
    • The entry into the vault on the shipwreck. Aside from the Timed Mission below, the infamous sunken ship panel has a reputation for being unintuitive in the extreme. Blow revealed in an AMA for Reddit that this was the puzzle he was thinking of when he off-handedly stated that "only 1% of players" would be able to solve it. It's a multi-layered, well hidden audio puzzle. It incorporates elements from puzzles all over the island, except mashed up to the point that realizing what's involved is half the puzzle. The bamboo forest's sound element is here, though it's part of the environment and not obviously artificial, leading some players to ignore it completely. The symmetry line from the ocean pillars is included as well, though it's invisible, and the colors that normally indicate its presence are muddled by a red light from the Greenhouse tinting everything.
    • The keep. The garden mazes themselves aren't too hard, but you have to remember the solution to all four puzzles in order to activate the beacon, two of the four at different angles from the original puzzle. The other side of the keep, with the pads you have to step on to activate, requires a similar mechanic to the garden mazes, but while the garden beacon at least follows the layout, the mechanical beacon does not, which means you have to follow the solution while remaining dead-on. Thankfully, only one of the puzzles, garden-beacon or mechanical-beacon, is needed to activate it.
    • For colorblind and/or hearing impaired players, there are two sections of the game which can be difficult, if not impossible, to complete. They can't be mentioned without spoiling the entire mechanics of the areas, but here goes, for those curious: the jungle area puzzles are based entirely on the audio pitches of birdsong, while the greenhouse bunker works entirely on manipulating colours of light to find the "true" puzzle. One puzzle in the keep also relies on audio cues to solve, and two additional (one in the hub/town and another on the shipwreck) run on recognizing how the audio cues work when translated to a geometrical representation — something explored in the jungle section. On this, Blow has said that he and his team ultimately decided to keep these puzzles intact, allowing the player to bypass them by only requiring seven of the eleven lasers to be fired the mountain in order to open it — which is alright, until one realizes that the endgame inside the mountain includes puzzles full of colour-based Interface Screw where solutions are required in order to finish the game. Color-blind players may also have trouble with the walkways through the trees, which are all about the different-colored suns. At one point, as many as five different colors are in the puzzle at the same time, and since color must match with color...
    • Most puzzles inside the mountain, including:
      • A set of puzzles with various Interface Screws, such as obstructive foregrounds, rapid panning and rotating, or the color-based ones mentioned above with flashing rainbow colors.
      • Puzzles whose solutions become Hard Light bridges that you have to cross. One has a blocking column in the middle, and the other couple are on opposite sides where you have to go back and forth altering the solutions until one of the bridges leads to the exit.
      • That column in the middle? It's filled with random junk, including puzzle panels that have to be solved from awkward angles.
      • A set of puzzles that are very easy by themselves, but are solved simultaneously, meaning they must share the exact same solution.
      • A nested puzzle, where a set of four puzzles become elements in a larger puzzle superimposed on top of them.
      • And the final area, where each puzzle is wrapped around a column, obscuring most of it from view.
    • The triangle puzzles leading to and inside the underground cavern, which the player receives no tutorial for, except for some hidden puzzles scattered around the map (which not only are hard to find, they're also much simpler than the puzzles in the mountain, which means you don't actually have practice in solving those unexpectedly harder puzzles, if you even managed to figure how they work at all).
    • The Challenge in the underground cavern. Where does one even start with this monstrosity? First, almost all of them are extremely tough. Second, there's over a dozen of them. Third, they're all random. Fourth, in at least two places, the location of the puzzle is random as well, one of these sections being in a maze chock full of shifting walls and blank panels (though this one is properly foreshadowed in another puzzle in the challenge). Fifth, in one section, you're given multiple panels to solve at once, in which only one of them can actually be solved; you have to figure out which one it is in addition to actually solving it. And the massive rotten cherry on top? It's all timed: if the music stops (or you pause), all the panels shut down, meaning you have to go back and do the whole thing over again. It goes without saying that by the time you actually manage to conquer this beast (and give yourself a huge pat on the back if you can), you will come to loathe In the Hall of the Mountain King with a burning passion for the rest of your days.
    • On a lighter note - there's one otherwise straightforward puzzle that involves a symbol that many people misinterpret at first glance. So many people have posted on the game's subreddit to ask "Why doesn't my solution work for this puzzle in the swamp?" that there's now an entire spinoff subreddit devoted to posts and jokes about the puzzle.
    • The fourth puzzle in the blue-with-red area of the swamp. By that point, the game has taught the player how hollow blue Tetris blocks work, and had only used them in singles in individual squares. Suddenly, the player is faced with a puzzle that not only features a 2x2 of them in one square, but within a puzzle that has very little room for all of the pieces to begin with without overlap. Is the answer to arrange them in a way that fits the field, subtract the 2x2 square, then rearrange the resulting pieces so that they all contain the four points needed? Nope! Apparently, adding to the swamp's Tutorial Failure on the main page, you have to overlap the yellow pieces. Solution spoiler  In all of the previous ones, one could easily interpret the blue square as being applied to a piece before laying them down, making room to fit, so long as the new square is in the overall shape. Apparently, you were supposed to overlap the pieces, then use the blue squares to cancel out overlapping squares and destroy any solo squares otherwise. Here's a link to a Reddit discussion which includes an easy-to-understand infographic to the logic behind the solution.
  • Underused Game Mechanic:
    • A criticism that's sometimes said about the game is that the environment is seldom integrated into the main puzzles. Most puzzles involve drawing a line across a panel depending on symbols written on it, with only some areas involving the world itself into the puzzles. The environmental puzzles are completely dependent on the world, but that doesn't prevent some people from thinking the panel puzzles are lacking.
    • The ⅄ symbol found in the quarry puzzles is seldom seen outside the quarry. There are four puzzles that use it: one in the ghost town, another in the windmill basement, another in the mountain ground floor (technically four, although they're all part of one, big puzzle), and another in the caves. That's it. The reason has probably to do with the way the game reutilises the symbols in areas different to the one that introduces them. In later puzzles, the game tends to combine several symbols to make more complex puzzles, or otherwise adding a gimmick that creates a variation on previously seen puzzles. However, by its own nature, the ⅄ symbol must be combined with other symbols, which means its introductory area already exhausted all possible ways to combine it with other symbols, and its reliance on other symbols makes more difficult to add gimmicks specifically designed around it, as opposed to more simple symbols that can easily have gimmicks.
    • Similarly, while tetrominos are used very often in puzzles, the blue, hollow tetrominos are seldom seen outside of the swamp (what's more, the swamp only uses them in the last puzzles). Again, only three puzzles use them: one in the vault near the desert ruins, another in an optional part of the treehouse area, and another in the caves. It's not clear why this happened, although a theory could explain it. It's been reported a glitch where, when pairing hollow tetrominos with the exact same number of solid tetrominos, the game automatically cancels them among themselves, without bothering to check if the shapes are also the same (as it does when the number of hollow and solid tetrominos isn't the same). This could lead to many unintended solutions, except that there was a good bit of Developer's Foresight, and existing puzzles involving hollow tetrominos are carefully designed so that it's completely impossible to even input such a solution. However, the presence of this glitch may have forced the developers to reduce the number of puzzles involving those glitched tetrominos.

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