Paper Mario: The Thousand-Year Door

Paper Mario: The Thousand-Year Door, released in Japan as Paper Mario RPG, is a console role-playing game developed by Intelligent Systems and published by Nintendo for the Nintendo GameCube. The Thousand-Year Door is the fourth game in the Mario RPG series and the second in the Paper Mario series.

Disappearing Punio/Invisible Punie Problem
In the second chapter during the Great Boggly Tree dungeon, you come across two adjacent cells (one contains the Punie elder, the other contains 90 Punies). After you receive the red key to open the elder's cell and attempt to open it, you will most likely come across a very frustrating problem: Punio will disappear and leave you stuck in a zoomed-in screen, hindering any further progress in the game. Many frustrated Dolphin users have been searching for a fix to this graphical issue, but seemingly to no avail.

There are specific revisions of Dolphin that WILL allow you to progress through this frustrating glitch: Dolphin IL, Dolphin IL and Dolphin IL. In these revisions players should find that Punio remains visible during the "cell-opening cut scene" and allows the game to continue normally. Unfortunately though, this revision does not fix another VERY frustrating problem: All but the main NPC Punies (Punio, Elder, Puniper & Petunia) will be invisible the entire time (only Punie shadows will be visible), making it very difficult to manage all 101 of them throughout the long dungeon. The framerate will also suffer a significant drop in this dungeon, probably due to the amount of Punies (well, Punie shadows) following you around.

Glitchy Toad/Pianta Problem
Near the end of the fifth chapter (right after the boss fight against Cortez) you find yourself forced to blow your way out of the Pirate's Grotto in the previous area before the boss which is filled with toads and the Pianta lovers. In most cases players will find that most of the toads (like the Punies in chapter 2) are invisible (only shadows). When you blow through the crack in the wall with Bobbery a cut scene plays, showing the toad next to the hole attempting to leave the cave and suggesting everyone else do the same. Now here this problem seems to vary depending on the specific build of Dolphin you're using, but in any case during the "escape sequence", one of the visible characters will suddenly start glitching back and forth and will halt you from progressing any further (you do not regain control of Mario until all the others have escaped).

Once again, only Dolphin IL, Dolphin IL and Dolphin IL  will work. However, in this case, even using these revisions the bug will still occur, but now you can get through this troublesome glitch continuously tap A until all of the characters have proceeded through the hole. In, the characters will still glitch back and forth for a short time, but will manage to unstick themselves after a short delay.

Corrupt Textures and other "Bounding Box" Issues
Some problems of texture corruption issues occur, see:

Sound Issues
Sometimes the background music isn't played or get the L and/or R channels desynced or muted. In extreme cases all sound in the game mute, needing to restart the emulator if you want the sound working again.

Testing

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Gameplay Videos
Paper Mario The Thousand Year Door on PC - Dolphin emulator