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.

Invisible X-Naut squad
In the prologue of the game, at the docks, when Lord Crump says: "It's go time!", many X-Nauts arrives but they are invisible with only their shadows shown. Refer.

Bad transition effects
When arriving at the docks and the boat turns around, the transition effect is bad. Also when entering pipes or other things, the effect is bad.

Disappearing Punio/Invisible Punie Problem
In the second chapter during the Great Boggly Tree dungeon, there are two adjacent cells (one contains the Punie elder, the other contains 90 Punies). After receiving the red key to open the elder's cell and attempt to open it, Punio will disappear and leave the screen stuck in zoomed-in, 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 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 around.

Glitchy Toad/Pianta Problem
Near the end of the fifth chapter (right after the boss fight against Cortez) one is forced to blow one's 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 one blows 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. This problem seems to vary depending on the specific build of Dolphin used, but during the "escape sequence", one of the visible characters will suddenly start glitching back and forth and will halt you from progressing any further (Mario can't be controlled until all the others have escaped).

Hatched Yoshi's Gulp action command not working
Upon acquirement of the Yoshi partner in Glitz Arena, he is required to complete the next fight against the iron clefts, With is ability gulp. However, the action command for it needs to be completed and does not work properly. it requires you to hold R and then release it upon reaching the end of a meter. The meter never fills, briefly flashes a full meter, and then fails. Thus pattern goes unaffected regardless of the mapped input and pattern of pressing R. Unfortunately, one cannot move farther in the game if experiencing this glitch.

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

Unknown Pointer Errors
When entering the sewers (in the prologue) the game crashes with "unknown pointer", this is addressed by using with DX9 plugin and default options.

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 to get the sound working again.

Testing

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