There are six endings in 999, each revealing its own pieces of information that collectively form the story. One of these endings is referred to as the "true ending," which ties everything together. It is recommended to experience this ending last, as it might otherwise reveal details you haven't encountered yet. The game can be played in any order, but to achieve the true ending, you need to have seen a few specific events in the game beforehand.

Please note that the names of the endings have been placed in spoiler tags. This is because they contain details that, well, could potentially spoil the events of those particular endings. You do not need to read the ending names if you wish to avoid spoilers.

The endings are decided by the doors you go through, with a few special events also playing a role. Ending 1 and 6 require specific events and are marked with an asterisk (*). Below is the order I personally went with:

1. Coffin - Door 4 → 7 → 1 *
2. Axe - Door 5 → 8 → 1
3. Knife - Door 4 → 7 → 6
4. Sub - Door 4 → 3 → 2
5. Zero Lost - Door 5 → 8 → 6
6. True - Door 4 → 7 → 1 *

The events you need to see to get ending 1 and 6 are the following:
1. Accept the offered bookmark after obtaining the tile from the display case.
2. Listen to the story about ice-9 in the freezer (choose "It did strike Junpei as rather odd").
3. Share the story about ice-9 in the operating room (choose "...Know about ice-9?").
4. Hand over the bookmark to Clover when you're about to leave the operating room.

Following this will give you all eight achievements from 999. The remaining 29 can only be obtained by playing VLR, the second game.

This guide focuses exclusively on door orders. In case you need guides on how to solve the puzzle rooms I recommend the ones uploaded by IGN as they are 100% spoiler free and easy to follow.

Feel free to leave a comment if you have any feedback or questions!