Hey there. This is designed to be a fully comprehensive Knytt Underground secrets guide. What does that mean, though? Well, in this guide, I'll be showing you:

• Where secret passageways are located (specifically in Chapter 3)
  
• What secret areas there are in each section (hub, chapter, even secrets within secrets)
  
• What achievements you can get through exploring secret areas

IMPORTANT: For ease of use, the map and its respective locations have been assigned X and Y points, with each points referring to a specific screen. The map (not counting secret areas) measures 48x30 screens, for the record. So (0,0), the top of the "graph", is located at the top-most and left-most screen of the overworld map. (47,29) is in the exact opposite direction.

Naturally, this guide has massive SPOILERS. Do not read past this section if you want to go into this game/certain parts of this game blind, or if you're looking for a challenge -- because believe me, some of these are damned hard. Without further ado, let's get going.

(Edit: It seems as though me and RarestMeow had the same idea. Here's to community!)

A secret passageway is simple -- just a hidden path between screens that can save you a bunch of time getting from area to area. As KU is both large in scope and has plenty of passageways, I'll be using the (X,Y) guide from earlier. If passages can't be entered from both ends, I will say so.
I will also be noting passageway clusters. Certain sections of the map have three or four different passages clumped between a few screens for various reasons. These will be underlined.

(However, I will only be using passageways that can be used outside of a quest or story. Secret passageways used for Niles' quest, for instance, won't be included.)
Without further ado, from the bottom....

(0,24): Located on the right, in the corner underneath the corridor. To reach this, go down one screen and activate the yellow orb, but cancel out of it when you reach this location. Going all the way down will allow you to reach a Disorder portal, collect a corner piece, and enter the Infinite Darkness. The reason I don't include the passageway from the opposite end is that it's impossible to traverse.

(5,23): Unknown, and possibly a coding error. This screen is a dead-end in Utopioca.

(15,6): In this dimly lit room filled with hieroglyphics, head to the right on the main platform. Don’t jump, though. Instead, go under the stairs in which you entered. This will allow you to pass under the platform and around, letting you obtain the Sun Triangle on the screen right of you.

(4,21): If you come up through the screen below, a passage allows you to access the string "bridge".

(1,14): This secret technically is useless, as it dead-ends a few screens from where it originates. It does contain a unique piece of dialogue from Cilia, though, and the entrance is one of the more difficult places to access in Chapter 3, as the center of the ceiling on this screen. The way to do this is after you give the flowers to Oldboard, so you can grab one or two green orbs on the next screen.

(16,7): Not necessarily a secret passageway, but going into the darkened passage on the left allows you to travel up a screen.

(3,21): This passage is only accessible through the challenge that starts at (5,20).

(5,18): Coming down from (5,16) allows you to enter the Temple area.

(9,21): By passing through the tower and down, you can enter the acidic area a screen below.

(4,13): You can pass through the left wall below the timed green block, basically allowing you to travel upwards for only an extra screen (and some nifty platforming).

(12,13): Going along the shadowed passage to the left allows you to access the top of the volcano area.

(18,12): Going inside the house will let you inside the smoky area, where you can pick up an item a screen above.

(19,10): This passage is only accessed through the challenge that starts at (21,9).

(5,10): You can exit out into the green area by going up past the top of the corridor and right. You can do this on the other side, but the wall jumps are difficult, especially on a keyboard.

(10,8): There's a section of the walkway with water pouring through. Go up the rightmost column to access the screen above.

(8,28): The passageway is located on the far right, allowing you to use a green orb from where you came.

(9,5): Along the bottom of the screen lie several "puddles". Entering two specific ones will allow you to drop down three screens below. As with (5,10), you can do this the other way around, but it's much more challenging.

(23,25): The building’s entrance provides the secret passageway down, going into the Esoteric Hideout/Web.

(1,3): A simple passage between houses on the right gets you to the other side of the smog-filled Tail village.

(16,19): There is an angular divot on the right wall. Entering it will get you a Dimension Crystal.

(2,0): This one's quite difficult. The main reason for this comes from the robot on the water, which can "see" you from a ways away, electrifying the water at an instant. First, jump onto the stalactite and grab the green orb. Then activate it, carefully navigating around the rock formations and the water. However, because the passageway is two screens away, you need to grab a second orb, of which there aren't any.
So, as you are activating the first green orb, turn and grab a second one while you're transformed. That way, when the first one runs out, you can continue on instead of plummeting into the water. Getting into the passageway nets you another corner piece and a Disorder portal. And no, you can't do it the other way around.

Continuing on....

(27,10): This is quite the difficult passageway to access, specifically located to the direct upper left of right “stalactite” (see that little divot in the ceiling? That’s where it is). To get here as I did, you must first travel a screen to your left by way of the blue orb. Then grab the yellow orb, jump down, and travel to the screen on your right (so that you’re located directly below (27,10)). With luck, you should be able to correctly align yourself in time to reach said divot, inside of which lies a coin.

(26,28): There are three small crevasses on the left wall of this room. The middle one acts as the secret passageway, guiding you towards a Dimension Crystal. If you continue left, though, you’ll find the Dub Dictator’s rave and similar goings-on. In fact, if you take the upper route in the Dimension Crystal screen, you’ll be able to go above his stage! (NOTE: you can also access this area from (19,28), by going into the oddly square-shaped hole along the upward pass.)

(33,23): Jump out and grab the green orb, activating it the instant it becomes available. Then, maneuver your way around and above the "spike", allowing you to grab onto the wall above. Moving left will take you to another item challenge.

(28,20): Passing through the house on the left allows access to the adjacent area.

(32,22): The passageway is located among the overgrown “hedges” to your right, along the wall. Jump up using the ball, and travel upwards, to an item challenge.

(37,24): At the far left lies a differently colored passageway, with bluish fog streaming in. This takes you to the next screen over.

(27,12): Not really a secret per se, but this one drops you down and right, near the first Utopioca exit. You can do it both ways, as the robots below are quite slow.

(42-45,25) Sewer Cluster: All of these secret passageways come from a series of rainy holes in the ground, and only two of them have any uses (a Disorder portal and an item challenge, if you go up on one of the screens).

(40,10): An obvious example. Jumping onto the column and into the house-like structure allows you to traverse up a screen, where a green timed button lies.

(43,23): In the background shaped like a thumbs up, enter the "thumb" and head right for an item challenge.

(41,20): The passageway is located to the left of the deserted house, accessible if you continue left, through the house itself. This allows you to eventually bring down the gate from the north entrance, in turn giving access to the needed green timer button.

(36,13): To the left of the angled platform lies what looks to be a hidden passageway heading up (which there is). Traveling up and left will take you to another item challenge. You can enter via the exit screen (35,14), but because it's well hidden within the ceiling, finding it prior to the other exit is almost impossible.

(36,11): Jump up to the left wall, and the passageway is at the very top. The next screen over contains an item challenge.

(46,28): This one's a bit of a doozy. To get to this Disorder portal and a corner piece, you must do the following: transform into a ball, immediately grab the red orb as you bounce up, then transform back and activate the jump at your highest height. Then transform back, gain momentum as the ball, and repeat. With luck, you should be able to reach the jutting ledge at the screen above. From there, go left.

(46,21): Transform into a ball above the flower with white and purple petals, and jump into the small dip in the ceiling. This will lead you to an item challenge in the screen above.

(40,13): On the screen below, grab the yellow orb and move up toward the lights. Jump off the one closest to the acid, and if you're fast enough, you should be able to activate the light, propelling you to a secret corridor. Entering it and moving right will net you an item. You can also reach (41,14), though this entrance is one-way.

(42,17): A fairly obvious one. To the left of the Disorder portal lays a hidden pathway, taking you to the screen below.

(42,14): This one is in the same area. Starting at (42,17), grab a green orb, and wait for it to respawn (you'll need two of these). Then activate the one you're holding and fly upwards. When that disappears, activate the second one, flying one more screen up and into the hole at the center of the ceiling. Inside you'll discover a stylized map of the Disorder. I wonder what achievement could be related to this....

(30,24): You actually start this at a screen below, with the red orb. Grab one, then activate it, propelling yourself up to the ledge with another one in tow. Then, climb up a screen, positioning yourself underneath the passage that looks like it could be secretive. Jump and activate the orb, hopefully landing you smack into the passage. With this, you can finally access that pesky room a few screens below.

(30,3): This allows you another way to enter the Shadowlands. Speaking of which....

(29-37,1-5) Shadowlands: There are eight secret passageways in this area. One of them completes a quest, three (well, technically five) grant you access into the area itself, one leads to an item, and three can lead you to the edge of the Underwater Lab section. Another one technically leads you to the nearby Bell of Fate, but it's blocked off by a timed green block.

(42,11): Jump up to where the horizontal pipe is, and go to the right wall up top. There should be a passageway to take you to a screen up, where an item challenge lies.

(37-47,0-7) The Underwater Lab: The Underwater Lab holds five passages. Four of them are designed as shortcuts (one actually dumps you out into the area below), but one gives you an item challenge.

(36,29): While not technically a secret, entering under the pipe coming out of the ground allows you to bypass the robots on the next screen, easily accessing a flower.

(40,9): The small divot in the rock allows you to access the area right of the mushroom village, without having to use the lights up top to deactivate the door.

(41,7) Pipe Cluster: This single room has three secret passageways going left, right, and down. Going up nets you a coin.

(46,9): Entering the lone house and continuing on allows you to access west of the mushroom village.

(44,10): You can do the same thing by entering the house on the right.

(43,1): At the save point, there's a grate on the right. You can enter it, but you might be wondering why you have to go up an impassable jump. That's because the entrance is at (46,2). For this, you need to do four things very quickly.
First, transform into the ball and build momentum by turning blue. Second, bounce down and grab the red orb -- as you bounce down on the next turn, angle your shot so that it hits the upper portion of the ramp. Third -- if aimed correctly, the bounce should aim you right at the walls above, where you need to transform and climb as fast as you can. Fourth and lastly, jump immediately and activate the orb. You should be propelled high enough to grab the ledges above. From there, you should find another Disorder portal and another corner piece!

Few metroidvanias are complete without secrets, and Knytt Underground is no exception. In fact, this game has so many secret areas that it might be the norm to the norm. Anyway, this section will cover:

• Where? (where each secret is (The Hub or Overworld))
  
• How to reach (reaching each secret)
  
• Result (what is it and what you find)
  
• Achievement? (if there are any achievements tied to said secret)

Now for the areas. Also, for those wondering what I mean by "The Hub", it refers to the area where you select chapters, view your achievements, etc.

Where? Overworld, at the save screen inside the temple within Chapter 1. This is the only secret area in the first chapter, so don’t worry too much.
How to reach: This might be one of the most annoying places to reach, in terms of timing. Regardless:
When you’re done collecting the candlesticks for Johann, go past the save point (and save) and out into the open. Normally when you go out, the column that helps you get in dissolves into the ground. This time, as you get far enough for the column to start dissolving, turn back and climb up the column. With your timing, you should be able to jump back up to the Temple’s platform, just as the column becomes too low to climb.
Result: The save screen is now covered by a massive black hole, as it seemingly sucks the light away. You can interact with it, but you can’t enter into it.
Achievement? Sadly not. It would be devilish, though.

Where? Overworld, in the Interlude. There are four interesting secrets in the Interlude.
How to reach: On the first screen, you’ll notice a crevice below the platform leading to the next screen. Enter it, and drop down.
Result: On the screen below, there’s a moon and clouds...for some reason. You can’t progress further, though.
Achievement? No.

Where? Overworld, in the Interlude.
How to reach: This one’s quite difficult. To even reach the starting point (a crevice at the top of the starting screen), you need to let the green button reach all eight bars. Then go up and quickly grab the yellow orb. If you don’t get past the green block reset in time, you have to restart the whole process over again. You have to book it to the first screen, and hopefully have enough time to activate the orb, traveling up to the crevice. This process will probably take you anywhere from 10-20 tries on your first go-around, so be prepared for a lot of restarts.
Once you’re in the crevice, travel up through a series of ledge jumps, and continue forward. By then, you should be able to figure out what to do next.
Result: You get two screens of secrecy. The first is beautifully lit with flowers, but if you travel below that, you’ll get one filled with small creatures, emblazoned with the words “HI PONTO”. Ponto is somebody known during the earlier days of Nifflas's forum website.
Achievement? No, but you get bragging rights, because I assume that less than 1% of players have ever made it to this area.

Where? Overworld, in the Interlude.
How to reach: On the screen with the two green orbs, you would normally use the second one to cross the chasm on the following screen. On the chasm screen, though, you may notice two “knobs” of space in the ceiling, and that’s where you need to use the second orb. Don’t worry if you disintegrate below, as you’ll simply spawn in the previous screen again.
Result: An entire starlit area, with several strange features (one of which is hidden within a wall). You may also notice that one of the screens holds the black hole from the Chapter 1 secret.
Achievement? Yes! Fireworks is obtained by completing an (entirely optional) segment of the area using only red orbs.

Where? Overworld, in the Interlude.
How to reach: This also employs the green orb screen, and this time you need to cross the chasm as normal. However, you should jump off the ledge overlooking the chasm before you activate the second green orb, because you’re going to need to go off the screen and up the next one (where you normally finish the Interlude). You can normally do this attempt once; if you can’t go straight up in time, you’ll be stuck on the opposite side of the chasm and will have to start over.
Result: There’s a strange area with glowing lights and a bright blue sky. Here, if left alone, Mi will dance eternally while a dance track plays in the background. Oddly enough, the drums seem to be sampled from Wolfgang Gartner’s “Yin/Yang” EP.
Achievement? Yes! If Mi is left alone to dance for a short time, you get the Dance In The Sky achievement.

Where? Overworld, in the Infinite Darkness, at (38,29).
How to reach: Underneath the weirdly shaped structure on the right side, move towards its base. You should be able to move into and beneath it, falling off the map.
Result: An expansive platforming challenge, with fifteen different challenges and brightly colored spaces. This is called The Figure (named after the software used for the background music in this area).
Achievement? Yes! Completing all fifteen challenges and returning to the overworld nets you the Falu Kohe achievement. In fact....

Where? Inside The Figure, during the Jobahifymo challenge.
How to reach: Pick up the green orb, then activate it. Move two screens to the left and one down, grabbing another one along the way. You should re-enter a screen with a large gap in its “ceiling”. Activate your second orb as soon as you can, flying out of the ceiling and to your left. You should drop down eventually, and once you’re on solid ground, walk all the way to your right.
Result: You should enter into a mysterious red forest, a place that you’re reportedly not supposed to be. Go on, walk around. It’s quite soothing. Music is by Harry Damm (D Fast).
Achievement? Yes! By entering in this area, you should get the Mysterious Forest achievement.

Where? Overworld, at (19,29), in the Infinite Darkness.
How to reach: There are three platformed columns on this screen, and the left one allows you to enter this area. Go under it and transform into a ball, building momentum to access the inside of this column. After that, simply follow the long path downwards, moving off the map.
Result: A massive village full of tails and sprites, hidden underground. You’re perfectly free to explore the area at your discretion.
Achievement? No.

Where? Inside the underground village, if you can believe it.
How to reach: On the lower right screen (the one with water streaming down), jump onto the rightmost wall and begin to build momentum as the ball. Then move off of said wall, bouncing up toward the streaming water wall. You should be able to climb up and to your left, before descending down.
Result: At the bottom of this secret (filled with lava stream and disintegrating infrastructure, you should find a green orb and a button. Activating the button, in turn, gives you access to another secret, which I’ll get to below.
There’s also another secret within this secret. If you grab the green orb and fly yourself to the topmost section of the screen above, you should be able to travel below the earthquake screen. Yes, this secret contains only a small screen with a few creatures moving about, but it signifies that even with all the desolation underground, life still finds ways to thrive.
Achievement? No. The related secret below, though….

Where? Overworld, at (38,28). This is directly related to the two secrets above, mind you.
How to reach: The earthquake you created seemed like it created another pathway to The Figure challenge from earlier, but if you drop down from this screen, you actually get taken to a passageway, leading you off the map.
Result: Another Figure challenge, this time called the Mini Figure. Instead of fifteen challenges, you receive only two.
Achievement? Yes! Completing the Mini Figure nets you the La Vupene achievement.

Where? Overworld, at (2,7).
How to reach: There are two raised platforms here, and you need to get onto the left one. Using your ball form, jump towards the divot in the upper center of the ceiling. With luck, you should be able to tuck yourself in it, and go left.
Result: Here, you won’t show up on the map anymore, but if you continue left, you’ll find a house with a woman out front. This is a bit of lore that I won’t spoil, but let’s just say that it has to do with a certain fetch quest early on in the game. Going further left will also dump you out at (45,18).
Achievement? Yes! You can get the Habanero Apologize achievement as a result.

Where? Just above the Infinite Darkness, at (30,26)
How to reach: On the upper left area of the screen sits a stalactite, where a right-facing divot is located. Climb into it, where it will take you left.
Result: In a tight passageway lies a large purple bird, presumably a duck of some kind. Continuing further dumps you out at (15,2).
Achievement? Yes! Going through this passage nets you the Redundant Bird achievement, though you might want to stand by it for a couple of seconds.

Where? Overworld, at (35,6).
How to reach: You see that slant on the top portion of the left wall? The secret area is within there. Simply jump, and climb up and to the left.
Result: This screen essentially functions as a “crossroads” within the Overworld, as there are two other spots within the map that you can traverse to (it is impossible, though, to return from whence you’ve came once you’ve dropped out). The right passage takes you to (8,24), and the passage down leads you to (44,22).
Achievement? No.

Where? Within the “crossroads” screen from above.
How to reach: As you enter the screen, go to the left wall, using the ball to grab on to the higher ledge. Hopefully, you should have successfully entered the secret passage.
Result: A fully-fledged art museum, complete with four floors and a robotic fairy tour guide. There are over 35 pieces of artwork around, and you most definitely aren’t the only creature present.
Achievement? Sadly, no.

Where? Overworld, in the Infinite Darkness, at (33,29).
How to reach: To do this, you must collect all four corner pieces from the map, and once you’ve done sol, return to this screen. Stand on the leftmost column, and use the ball form to jump into the passage directly above it.
Result: A…sandwich recipe entitled “Katie’s Foot”, courtesy of an icon on your HUD. Scrolling over it brings up an honest-to-god, complex, and seemingly delicious list to make an entirely unique dish.
Achievement? Yes! Doing this nabs you the Sandwich achievement.

Where? Overworld, just below the Great Artifact area at (23,20).
How to reach: This screen is incredibly unassuming, so you’d be forgiven if you completely bypassed this secret. To reach this passage, located in the sunken hole of the screen’s ceiling (on your left), you need to do the following three actions:
First, transform into the ball and build momentum on the raised platform to build momentum. Second, while still as the ball, jump and bounce off the right slanted wall of the hole. For the third step, though, you need to quickly shift to the left and bounce off another slant, this time on the right side of the raised platform.
It might seem odd, but it works.
Result: Another art museum, run by a fairy named Ethan (whom you actually meet in the game’s demo). While this one is considerably smaller (the previously mentioned museum has five floors, and this only has two), it’s still an enjoyable diversion.
Achievement? No.

Where? The Hub
How to reach: Go to the title screen, then left and down a screen each. To the right of the “pendulum” weight is a part of the wall jutting outward. Jump onto it and climb upward, and once you’re inside the wall, you should be able to fall straight downward.
Result: A hazy alcove screen with a purple teleport in the middle, which will surprisingly take you to the Knytt Underground debug area. The debug area is called "Chowdren" by Nifflas' avatar (because he assumes that you are the developer porting the game, specifically named Mathias), but there may be no official name at all.
Achievement? No.

Where? The Hub, within "Chowdren".
How to reach: When in the top-leftmost screen, climb all the way up the top of the left wall, and go left.
Result: Three large sprites from Nifflas’ two previous games in the series. There's Juni from Knytt Stories, the original Knytt from the first game, and a green-clothed Knytt that's also apparently from the first game.
Achievement? No.

Where? The Hub, on the screen that leads to "Chowdren".
How to reach: On the level where the teleport is, enter into the right wall.
Result: A bright clearing, where in the center lies a crude yet cute drawing of a sheep.
Achievement? Yes! This brings up the Because It’s Tradition achievement, because this drawing apparently shows up in every game that Nifflas had worked on up to that point (tribute to Jace Greywool).
(There is also another secret that leads directly off of this one, though it’s for aesthetic purposes only. Climb all the way up to the top of the right wall in the aforementioned screen, and you should be able to enter a secret passageway that travels below, to a screen where the walls spiral inward to the center.)

Where? The Hub, in the Chapter 1 area.
How to reach: On every screen where you delete chapter save data, you may notice a very small ledge directly above the deletion prompter. This doesn’t do anything for Chapters 2 & 3, but for Chapter 1, attempting to climb up there will get you somewhere else.
Result: This drop you out onto a four platform pedestal, and traveling right will allow you to teleport to a secret (non-canon) segment of the game, which is titled A Toast (named after the song that plays in the segment).
Achievement? Surprisingly, no.

Where? The Hub, on the screen that takes you to the Achievements, Demo, and Credits.
How to reach: The screen is mainly featureless, save for a column in the middle. Get situated on the left side of the column, and jump towards the exact opposite wall. It may take you a few tries, but once you’re there, climb up and to the left.
Result: Two separate challenges named after different word fonts, Comic Sans and Papyrus. Each one strips you of your sprite/ball form, respectively, and tasks you to travel to a specific location in the Overworld.
Achievement? No, but I speak from experience when I say that both challenges are fiendishly difficult, especially if you don’t have any idea where you should go. Consulting a guide is highly recommended, even if you're an expert.

Where? The Hub, during the Credits section of the game.
How to reach: The Credits area is a unique one. As opposed to most other video games, where you just watch a scrolling “movie” with the names of those who worked on it, here Mi traverses her way through several screens of credited names. You might notice several platforms located near the ceiling, and this is where the secret comes into play. It’s difficult, but if you accomplish it, you’ll be able to move in a different direction on the third screen.
Result: A screen that teleports you to Juni’s house, where you actually play as Juni for a short while (as narrated by Nifflas’ avatar). This story seems to be called Juni and the Missing Puzzle Piece.
Achievement? Yes! Entering into this secret will net you the aptly named Knytt Stories achievement, as Juni is the protagonist of said game (and one I highly recommend).

Where? Inside of Juni’s story.
How to reach: When starting out, travel down a screen, and enter into the underground section (technically down two screens from where you began). From there, jump onto the part of the wall in the middle of the blue stone background, and climb.
Result: A screen with plenty of pulsating lights amid a darkened screen, kind of like a dance floor. If you let Juni be, she’ll begin to dance.
Achievement? Yes! Allowing Juni to dance for several seconds gives you the Tobias Chilli achievement.

Where? The Hub, by Chapter 3.
How to reach: Unlike Chapters 1 and 2, Chapter 3’s teleporter (or whatever you want to call it) is located on a freestanding platform. By this point in the guide, I think you probably know what to do ;).
Result: A completely hidden corridor that travels further and further away from the Hub. There are also two buttons that respectively mute the ambience and your footsteps, and the resulting area called Neon Falls is an “epilogue” of sorts to the main story.
Achievement? No.

Where? Inside of the Neon Falls secret.
How to reach: At a certain point, there’s a segment in Neon Falls (after the beats begin) where the background of the map turns magenta. Or, if you’re color-blind, It’s just after the robots stop appearing. Regardless there’s a divot that seems longer than usual on the right wall, partially obscured by a leaf. That’s the secret path to take.
Result: An entirely new secret area, controlled mainly by rhythmic “lava”. The song in the background also changes, too.
Achievement? Yes! Completing this new gauntlet grants you the Pew Pew! achievement, relating to the indie game LAZA KNITEZ!!.

Where? Inside of the Neon Falls secret’s secret.
How to reach: On the first screen where the rhythmic “lava” appears, go to the left side instead of the right, and climb the wall/use a quick ball transformation to jump into the ceiling.
Result: Several screens of wholly lava challenges, completely with a blank background and spartan design. The contrast to the rest of the secret area’s aesthetic makes it memorable, if short.
Achievement? No.

Where? Also inside of the Neon Falls secret’s secret.
How to reach: On the specific screen where the red light power-up is located, you might notice that the center wall is shaped like a capital L, with a small pit branching off of it at the bottom. Jump (or use the red orb) to the top of the “L”, and you can climb inward.
Result: The third and final Figure challenge, this time named Tiny Figure. Funnily enough, this one is slightly larger than the Mini Figure, having three challenges to the other’s two. Completing this will teleport you back to its entrance.
Achievement? No.

Where? The Hub, below the Chapter 3 screen.
How to reach: Where you drop down into the pathway that eventually takes you to Neon Falls, just jump off of the left platform onto the wall next to where you came in, and climb.
Result: An entirely hidden challenge entitled HUMLab Murder Mystery. The styling is much like the Figure challenges, though.
Achievement? No.

Where? The Hub. Actually, it's inside the place where the HUMLab Murder Mystery is.
How to reach: Just go to the left wall of the small screen, and begin climbing.
Result: An oubliette-like space. Fitting, since it’s one of the most hidden areas within the Hub. This takes you to yet another challenge entitled Sync Transform, where you’re tasked with…well, I won’t spoil the fun.
Achievement? No.

MAJOR AREA SPOILERS FROM THIS POINT FORWARD

Where? The Hub, at the chapter selection screen.
How to reach: I’m actually not going to say how to reach said secret, because it’s fairly obvious.
(To those that are especially stuck, though, here’s a major hint. Do you know how, when you climb up towards Chapters 2 and 3, there seems to be a middle passage? Well, how do you get there, specifically?)
Result: An entirely new upper section of the Hub, with plenty of new places to visit. Upon a closer examination, though, I wonder if Nifflas had more areas in development, but scrapped them as time continued. Knowing that the entirety of the screen space for the game was completely filled out, though, this isn't likely to be the case, unfortunately.
Achievement? No, and from this point on, there are no more achievements to obtain.

Where? The Hub, within the upper area.
How to reach: Simply go left a screen, once you reach that area.
Result: A new area guarded by a Tail, who asks you to please finish Chapter 3 before you progress (I’d recommend his advice). The resulting area is called A Stranger Dream, in reference to Knytt Stories’ “A Strange Dream” episode, and the whole experience is a bit odd. (There is a secret passage in this adventure, located on the fifth screen and to the left. However, all it does is transport you to a slightly further area.)

Where? The Hub, located a screen past A Stranger Dream.
How to reach: On the screen where you begin said area, simply climb upwards.
Result: Situated on a tall column lies the RPG Story, a tongue-in-cheek "RPG" experience which features plenty of merciless mocking by Cilia. Definitely worth a play.

Where? Inside of the RPG Story.
How to reach: There’s a section on the map, where you can see an acid flow entering from the top and exiting below where you walk. There’s a crevice on the right wall, which should be fairly obvious. Enter it, and go right.
Result: Much like the Tobias Chilli achievement mentioned earlier, this passage takes you to a dimly lit screen with many pulsating lights, so that the hero can dance to them. However (and I believe this only counts for those who either haven’t downloaded the Infinity Hype update or are playing on older systems such as the PS3), this actually counts as an achievement entitled Heroic Dance.

Where? The Hub, also past A Stranger Dream.
How to reach: There are two other secret areas here. The first is a screen left of A Stranger Dream, accessed by jumping into the constantly pulsating black squares. The second is left to that one, on its own small platform.
Result: The former is a challenge called Void Pointer, named after the artist whose track plays in the area. To give you an idea of how difficult this place is, it’s akin to the Sync Transform challenge, except that you’re stuck in ball/sprite form depending on the music. Good luck.
The latter has a much more laid-back atmosphere, and is titled Ask Knytt Underground Characters (more often Nifflas’ avatar than not). Like A Stranger Dream, this area poses quite a unique experience.

Where? Within Ask Knytt Underground Characters.
How to reach: Once you’re transported to that area, simply walk to the left off the platform and into the nearest wall.
Result: The ensuing corridor allows you to bypass the first three sub-areas, dumping you out just before the fourth one.

Where? Within Ask Knytt Underground Characters.
How to reach: This is another opening, on the right wall above the fourth sub-area. If you used the previous secret passage, just drop down to the wall next to you, and you should be able to enter easily.
Result: The other passage in this area allows you to skip the last two sub-areas (not including the fourth one), going straight to the end screen. On the screen with the last sub-area (with the question mark as the sign), you can travel upwards to a dimly lit screen. In the center of it floats a pinkish ball of disorganized lights. What representation this has, though, I’m not sure.

Where? The Hub, within the upper area.
How to reach: Simply go right a screen, once you reach that area.
Result: Surrounded by four small pedestals lies a new challenge area, titled Anti-Figure. I have yet to play this fully, but it definitely looks like it requires plenty of focus.

Where? The Hub, at the screen containing the Anti-Figure.
How to reach: If you’ve been to the Anti-Figure area by this point, you’re probably wondering what purpose those small platforms surrounding the entrance do. Well, try latching onto the walls of the top two, and jump upwards.
Result: A screen devoid of natural life, unlike all the other Hub areas. Instead, this one happens to be filled with several large tires and streetlights.

Where? In the secret mentioned above.
How to reach: Simply travel to the left wall, and climb all the way upwards.
Result: A small screen not far from its entrance, enveloped in a blinding light. If you touch its center, you’ll be able to transform into your ball form within the Hub! (You won’t be able to reset your forms until you restart the chapter select option, though.)

Where? Within the screen containing the RPG Story.
How to reach: On your first go-around, you may have noticed a plainly obvious passage on the top left. When you’re in your sprite form, this place is impossible to reach, but not in your ball form.
Result: Dub Dictator has returned to give another performance, this time smack in the Hub area (of all places). You can no longer go above the stage, but you can still keep enjoying the music. Interestingly enough, this area provides the background image for the Knytt Underground OST on Bandcamp.

Where? The Hub, left of the title screen.
How to reach: This is probably the most difficult and obtuse area to arrive at in the entire Hub region (or even within the entire game), and I admittedly entered into it by accident. Anyways, return to the area where you could access both "Chowdren" and the sheep drawing. Instead of moving to the right, jump towards the ledge on the left.
Result: A small area similar to the rest of the Hub, filled with small platforms (there may be some interactive pieces there, but I’m unsure). Dropping into this place will transform you back into a sprite, and if you travel left instead of right, you’ll be greeted by one of the most unique areas in the entire game. It’s comprised of only one screen that’s filled with a colored light, bearing one short sentence in the center. I won’t spoil what it says, but it sums up the entirety of this guide quite succinctly.

...There is actually one final secret, located within the RPG Story.
On the screen where you obtain the sword, you'll notice some ledges leading upward. Despite its seeming impossibility, you can actually climb up to the screen above via superhuman precision. If you enter the screen on the right, though, you'll simply find a purplish screen where your heroic protagonist will fall forever (until you return to the chapter select, that is). While it looks like a glitch/out-of-bounds screen for the game, it was deliberately placed there to fool people into thinking that it is one.

Special Thanks
May I just give a special shout-out to the following people:

• MrVuule for providing videos on certain achievement pathways, which I had forgotten about (this took me about seven months to complete). If anyone has trouble visualizing certain achievements to get to, simply check out their videos.
  
• vsd over at Nifflas’ Support Forum, for providing me with the proper names for many of these areas.
  
• Of course, Nicklas Nygren “Nifflas”, for being the impetus and driving force behind the beautiful game.

Credits
This guide was created entirely by DrNagamiyaTenma (myself) from July 2020 to January of 2021, using resources from the Knytt Underground community at large.

Update (06/13/2021): Because of the comments made by Kilicool64, I've changed plenty of the formatting throughout the guide, and included one last secret within the guide's final section.

Update (03/18/2022): I edited some spelling errors and changed a bit of terminology around due to differences in the game files.

If you have any questions or advice to give to me, please don't hesitate to do so. I will be happy to hear it. Thank you for taking the time to read this guide.