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In the game's data, found at the offset 0x32E of it's ROM are the strings "MINATO", referencing Minato Giken, the developer company that worked on the game.

In the bonus co-op mode Half-Life: Decay found in the PlayStation 2 port of the game, the ending of the mode can be seen from the perspectives of either playable character in the game, Gina or Colette. If you see the ending from Colette's perspective, a brief shot of a broken computer can be seen with red electrical arcs shooting out of it. Connecting this arcs in an emulator reveals the initials "MA", the signature of Gearbox Software level designer Matt Armstrong, and a symbol that he would often hide in games he worked on.

There are eight hidden developer credits that when entered into the High Score rank board will cause that row to display a flashing rainbow effect:
•KISSY = Yoshihiro Kishimoto, Programmer
•TAKKY = Yukio Takahashi, Designer
•MAKO. = Satou Makotoshi, Unknown Role
•JUNKO = Junko Ozawa, Composer
•YURI. = Yuriko Keino, Composer
•FIGER = Unknown
•NKGT. = Norio Nakagata, Composer
•WATAB = Unknown

In 2021, several cheat codes were discovered in the Game Boy version of the game, the first two of which must be activated through the title screen.

•Ending and Credits: Up/Down/Left/Right/Select/Start.

•Sound Test: Down/Up/Down/Up/Select/B.

•Level Select: While paused in normal gameplay, press Down/Select/Up/Left/Select/Right/B. Press A or B to select a level.

•Hidden Tribute to Hiroko Kasahara: To access it, you must first access the Sound Test menu. Then, set the BGM/SE index to 02 and press A once, then set BGM/SE index 19 and press A once more. Lastly, you must input the following lengthy code:
Up, Up, Down, Down, Left, Left, Right, Right, Select, Select, Up, Up, Down, Down, Left, Left, Right, Right, B, B, Up, Down, Left, Right, Select, Up, Down, Left, Right, B, Select, Right, Left, Down, Up, B, Right, Left, Down, Up, Select, Select, Right, Right, Left, Left, Down, Down, Up, Up, B, B, Right, Right, Left, Left, Down, Down, Up, Up, Start.

If inputted correctly, an alternate credits sequence will play out. The normal credits plays the game's ending theme and lists the name of programmer Yutaka ★Hiroko★ Sakashita among the game's developers. This alternate credits sequence instead plays the Vs. Mode music and lists the name Hiroko Kasahara at the top of the screen. Kasahara is a J-Pop singer, and the names of the game's developers in the credits are replaced with a comprehensive discography featuring the names of several albums she had released up to 1993, including the release dates for her then-upcoming 1993 albums "L'Express Fantasie" and "Nature". Considering Sakashita used Kasahara's first name on the standard credits sequence, he is most likely the one who included this Easter egg to document his love of her music at the time the game shipped. The fact that this sequence is hidden behind two cheat codes that would take almost 30 years to be discovered, with one of them being too long to easily guess, suggests that it was never meant to be seen by players.

In 2022, an Easter egg was discovered after one of the game's developers hinted at its existence in the game's Discord fan server. In the Ungard Mines level, when you come to the big bridge, you can turn to the left to find two bags of gold. Pick up the first bag but leave the second bag alone, and then carefully walk to the end of each of the four diagonal support beams holding up the bridge. Afterwards, on the opposite end of the bridge, walk to the end of the carved out rock path on the left side and stand in the corner of the rock wall. If done correctly, the "Use" prompt should appear. After triggering it, you can turn around and see a developer credit written in magical colored lights hanging over the abyss: "J.A WAS HERE". This is in reference to one of the game's designers Jens Anderssen.

A pair of unused text files featuring an abstract of the game's plot and a short list of developer credits can be found in the game's data:

•abstract.txt:

THE APPRENTICE
This is the story of a week in the life of the
wizards apprentice, Marvin. You must successfully
complete the tasks set for you by Gandorph S.
Wandburner. This will take you to many different
places and you will have to solve various puzzles
and defeat numerous enemies to accomplish your tasks.

•bibliographic.txt:

The Apprentice
Programming by Tim Moss
Graphics by Luke Verhulst
Game design by Luke Verhulst and Tim Moss
Music by Joost Egmond

A 1994 Vision Factory production in cooperation with
Philips Interative Media inc.

In the European release of the NES version, pressing Right on the logo screen for the game's publisher Storm will trigger a secret set of credits menus. This screen can also be accessed during any cutscene by pressing Right after the message at the current cutscene is displayed and the program is paused before the next cutscene screen and waiting for the input to skip it. This occurs because the input waiting routine is the same for the logo and for the cutscene waiting screens. The Japanese version of the game has no starting logo and the cutscene input logic is changed, but the credits are still in the game and can be accessed through hacking.

Entering the cheat code "UGLYMUGS" and viewing the game's credits will display a group photo of the game's developers, Left Field Productions.

If you explore Level 50, you can find a game developer named Dane in a closed off office-like space where he will say that the player can stay as long as they don't do anything to his computer as he is working on the game as the player is playing it. If the player does end up raining on the computer then they will get abruptly booted to the title screen.

In the "Disco" Arcade mode map, a record can be found on the mixing desk featuring the artist "Norgatious G". This is both a reference to the band Tenacious D as well as TimeSplitters' series composer Graeme Norgate.

In 2021, an anonymous Xbox developer informed Kotaku of an undiscovered developer credit on the Xbox. To find it, insert a music CD, and from the Audio CD screen choose Copy, Copy, and then New Soundtrack. Delete the default soundtrack title and replace it with the following name (without quotation marks): "Timmyyyyyyyyyyyyyyyyyyyyyyyyyy!"

Wait for the CD to finish ripping and then return to the main menu. Now going to System Info within the Settings will reveal an updated screen crediting the four programmers that made up the Xbox Dashboard Team.

A lengthy hidden developer credit for all those who worked on the Xbox console can be found by inserting a music CD, going to the Audio CD menu, selecting and pressing Copy, Select All and then Copy again. You are then taken to a menu to name the Soundtrack you have just selected, where you should enter the following name without the quotation marks: "[two less-than symbols]Eggsßox[two greater-than symbols]"

When you hit Done, the Xbox loading screen appears and will take you to a credits sequence, thanking the developers who made games for the Xbox and their playerbase before giving thanks to The DirectX Team, Microsoft Hardware, Worldwide Operations, The MSN Gaming Zone, Windows Core, and the entire Xbox Team and their families for tolerating the long work hours it took to create the console. The credits end with "XBOX 2001".

In 2021, a widely undocumented easter egg during the "Enter the Battle Dome" mission in "The Umpire Strikes Out" level in the Rocket Channel was uploaded to YouTube. When the player reaches the purple energy tower, you will need to climb the tower up to the square platform area with two air tanks on it. Just to the right of those air tanks, an invisible path marked by vague star textures and small red lights will appear in view once reached, leading to a hidden area with a floating metallic cube featuring a photo of programmer Evan Wells behind a blue background. Like the production baby cameo found in the same level, the object will slowly spin around showing the photo on each side, can be jumped on, and can be destroyed with Gex's attacks.

In 2020, a widely undocumented easter egg near the start of "The Umpire Strikes Out" level in the Rocket Channel was uploaded to YouTube. From the level's checkpoint, there is a platforming section consisting of floating metallic walkways. If the player karate kicks from the second walkway into the abyss, you should land on a mostly invisible platform, only marked with vague star textures and small red lights. Going south of the platform will lead the player back to the start of the level. If the player goes north, mindful that you jump over a hole in the platform on the way there, a small area can be found that contains an oxygen tank, some crates, two Green Fly TVs, and a floating metallic cube with an image of a newborn's face on two sides. The cube will spin in place slowly unless the player destroys it with Gex's attacks. The cube even has some collision that allows the player to jump on top of it. It's unknown who this infant is, but it is presumably a production baby raised by one of the game's developers.

At any time before the story ends and when the entire map is unlocked, if the player tries to fly or boat out of bounds and away from the map they will trigger a secret ending. Spoiler:Specifically, when the player passes the boundary the screen will fade to black with "3 Months Later" displayed. The scene then cuts to one where Dani is lounging on a beach with a radio next to him where negative news involving the events on the island and around the world can be heard. The Radio then starts playing Congo by Gloria Estefan which continues into the game's credits. This is the only way to get the "Hidden in Plain Sight" achievement/trophy. However, all of this will not work if the player has beaten the main story.

In Chapter 9, in the library, there are books with the snail logo of Tango Gameworks, the developer team that created the game.

In the original game, the mural in Hyrule Castle Town was blurry and hard to make out. In Twilight Princess HD, the textures were updated with clearer, brand new designs. Notably, this updated mural features a Rito, a species which does not exist at the time the game takes place nor in the series' Child Timeline.

Separately, in the Temple of Time, a picture frame can be found with a backwards message written in Hylian along the lower border. Translating it reveals a hidden developer credit: "Jack Kirby Crosby Made This".

Crosby, a graphics designer working for Tantalus on the HD remaster of Twilight Princess, later confirmed that he was responsible for both that credit and the mural, the latter of which was the result of a higher-up at Nintendo asking for some reliefs in Hyrule Castle Town to be redone in the same style as a shop he had re-textured. The new mural design was inspired by Crosby's own idea of a story for a Zelda game and drew additional inspiration from a Zelda art book without any story direction from Nintendo, meaning the events depicted therein are non-canon.

Upon completing the game on Extreme Difficulty, the text that would normally say "Thanks for Playing" is replaced with one that says "Dream and Friends", referencing what was said by Scrooge to his nephews in the ending of the prototype version of the original NES game.

Upon catching a squid, the message that pops up will say that it's "off the hook", referencing the duo Pearl and Marina from the Splatoon series.

Although the game takes place at Disneyland in California, the book that Mickey Mouse signs an autograph on is actually from the park's Florida counterpart Walt Disney World, as evidenced by the exclusive park attractions.