

Game always sounds broken after every cutscene and the only way to get rid of it is to save and load, often triggering another cutscene
Cutscene audio will keep playing and loop every second to create an awful audio sensation
The cutscenes had audio after deleting my prefix once. The new audio issue is way worse

Tried all the fixes listed on ProtonDB but none actually worked to bring the cutscene audio back
Installed LAV Filters
All cutscene audio is missing
Cutscenes are a vital part of the game's story. Unplayable in this state imo

Videos (and their audio) only work as expected using Proton 6. I've tried GE and Experimental, and they all present some issue or another with the audio in the videos. Only Proton 6 was able to work as expected.
Using these settings:
- Render: OpenGL
- Window Mode: Borderless
- Vsync: On
- Anisotropic Filtering: On
- Anti-Aliasing: MSAA (16x)

Installed LAV Filters 0.79.2
TDP 8
Launcher required mouse control, graphics config required switching to desktop mode
Cutscene audio fixed with combo of GE version and LAV filters
Other suggested versions either resulted in broken video or audio in different cutscenes. This followed a lot of trial and error so some intermediate step may have had an impact.
Use Proton 6.3-8 and install lavfilters via Protontricks. This has fixed the cutscenes in the first game for me.
The graphics sub-window has no [X] button to close it, so you need to use [Steam button] -> [Close window] to get rid of it.
Cutscenes' audio is missing unless you do the mentioned tinkering.
had to switch to poton ge 7-17 to avoid crash in VLR

Need to change graphic options between games and video scenes won't work without further tinkering
Some animated sequences won't play
VLR game crashes if it is not launched with opengl
It works great but you have to change graphic options (opengl) when playing VLR (the second game in this bundle) because without it, the game crashes all the time to the point where you can't progress a entire puzzle without the game crashing.
The game is compatible with texthooker, so great for learning japanese too.

Only tried so far 999 with ProtonGE9-1 Borderless 2560x1600 Direct3D9 MSAA 16x
Didn't notice any problem so far, sound and videos work

gamemoderun mangohud %command%
- [999] One specific sound effect (door closing) sometimes loops infinitely. Only way to fix is to save, return to title, then load. Some sounds are supposed to loop (footsteps) so don't be confused about that.
- [999] Mouse cursor flickers while moving.
- [VLR] Mouse cursor flickers and changes to your desktop cursor while moving.
- [VLR] Direct3D9 renderer crashes with GE-Proton during certain transitions (e.g. opening the save menu). Switch to OpenGL renderer in the launcher. Doesn't crash with Proton 8/Experimental but then you won't have video.
- [Both] Videos don't work with Proton 8/Experimental. There is no indication, it just skips to the next scene/dialogue instantly, so you might not know you were missing videos if you have never played the games before. Note 999's first video is after you start a new game, while VLR has a trailer video upon launching the game (after logo, before main menu). Videos work with GE-Proton.
There are two games (999 and VLR) so I've marked each point accordingly.

gamemoderun mangohud %command%
One specific sound effect (door closing) sometimes loops infinitely. Only way to fix is to save, return to title, then load.
Audio is very unbalanced, not sure if that's Proton/Linux-specific. I have to set music to 4, SFX to 8 and vocals to 10 to get something normal sounding.
Mouse cursor (not WASD/joystick cursor) flickers when moving
Videos don't work with Proton Experimental (8.0-20240111c). There is no indication, it just skips instantly, so you might not know you were missing videos if you have never played the game before. There should be a short intro video when you start a new game.

The launcher only supports touch. You can not change launch settings as the pop-up can't be closed.
Videos are not playing which makes you miss vital story. Had to finish the game on Windows instead.

Perfect OOTB
Only tested 999, not VLR (it's two games in one)
GPU 200, Framerate Limit 60, Half Rate Shading
videos sometimes had some compression artifacts, though that could be in the original game.
Notes don't work well on the steam deck. Though Steam Deck is adding an official notes feature soon, so that won't be an issue once that happens.
Crashed 1 time
It only runs on Proton-6.21-GE-2. Would not start on any other version of Proton tested.
The opening movies don't play audio but that has no impact on the gameplay.
The first game "999" runs fine but the second game "Virtue's Last Reward" crashed for me as long as I wasn't using the GE 7-17 version
Requires touch screen to select game in launcher
Writing notes on VLR with touch screen is very imprecise
Opening FMVs don't play
GPU 200, Framerate Limit 60, Half Rate Shading
videos sometimes had some compression artifacts, though that could be in the original game.
It only runs on Proton-6.21-GE-2. Would not start on any other version of Proton tested.
Was able to play both 999 and VLR
videos dont play when using proton 7.0.6; using proton ge plays the videos but without sound
Launcher needs using touchscreen navigation
Only 999 was tested at the time of writing this report and works fine, though cutscenes are not played unless you are using Proton-GE. Still, is completly playable using official Proton.
Virtue's Last Reward has working FMVs with 6.21-GE-2. Other Proton forks will either skip them or play without sound
Need to close graphics settings window via Steam menu
I didn't test each game extensively but I can at least confirm VLR's FMV issue is fixed, with the only slight bug being a sound hiccup just before an FMV plays. 999 exhibits similar behavior, and it too has working FMVs, so I recommend just leaving it on 6.21-GE-2 for consistency unless it breaks something else.
Virtues Last Reward does not play, but 999 plays perfectly well.
Had to use touch to change settings
No audio in videos
The game works fine without any changes. Just the videos are not working. I had to change to Proton GE to get those, but the audio in them is still missing. But this has minimal effect on the game.
protontricks 477740 lavfilters
works fine with TDP set to 3
Laucher works at lauching both 999 and VLR, but video settings has to be changed through Steam Deck "Desktop mode".
999 and VLR works fine with latest proton versions but videos don't play(at least for 999), used protontricks lavfilters and switched to proton 6.3.8 and videos started working. unsure if changing only proton version fixes or you also need lavfilters. Played both games and never had problems and all videos were playable with fixes I've listed.

The games setup tool you have to use the touch screen and can't back out of the menu so you can't setup options.
Both games in this bundle work fine without changing any options, haven't played with options on desktop, so not sure if the second game could look better. First one is perfect on default.
Options must be shutdown via Steam button>config windows>X button.
Sometimes, the speech disappeared.
Without setting the GE 6 version, VLR won't launchh as for now.
protontricks 477740 lavfilters
works fine with TDP set to 3
Laucher works at lauching both 999 and VLR, but video settings has to be changed through Steam Deck "Desktop mode".
999 works fine with latest proton versions(which I used mostly) but videos don't play, used protontricks lavfilters and switched to proton 6.3.8 and videos started working. unsure if changing only proton version fixes or you also need lavfilters. Tested the first 15min using this version so unsure if there any issues later.
Didn't test VLR yet...
Changed right trackpad to left mouse button click so i could more easily start the launcher menu without using the touchscreen.
Video options doesn't close on its own, you need to press the steam button and close it manually.
crackled when resuming from standby mode
Virtue's last reward doesn't launch at all.
Videos don't play during 999's intro or when entering or leaving escape rooms.

Chose OpenGL as the renderer
Needs 2 different proton builds. 999 Runs in the latest Experimental Proton while for VLR you should install Proton 5 to be able to get to the main menu and play it, otherwise it will hang after the Spike Chunsoft logo.
Text in the launcher shows as squares using Proton GE (this does not occur with Proton Experimental).
Videos (doors opening/closing, trailers) did not play in 999 with Proton Experimental.
The launcher works fine, but the Settings subwindow is too large for the SteamDeck. The Close button is out of reach and forcing Escape or Steam+B doesn't close it. However, you can configure that in Desktop Mode and ignore afterward.
Absolutely perfect for both games except the sound for the intro cutscene of Virtue's Last Reward as well as the short "Find a way out" and "You Solved It" cutscenes. Those videos work and don't crash or anything, there's just no sound. By no mean this means the game isn't playable, this is a nitpick I wanted to mention.
Remember this is a compilation of two games : 999 and VLR.
999 can be played with the default Steam Proton without tinkering. First time players have nothing to worry about.
VLR need GE. As of 7-17, it works perfectly except for the missing sound during videos in VLR (there are none needed for the story, it's just two 2 seconds cutscenes and the intro leading to the title screen)
Unable to close the video options in the launch window.
Must use GE Proton 7-14 to play Virtue's Last Reward. It will not run otherwise (black screen).
Works perfectly out of the box
Works flawlessly

6.12-GE-1 GloriousEggroll
Installed "quartz"
Annoyingly, videos now skip and refuse to play at all. When a door opens, it will skip to it being open. I have not played the entire game yet, this may cause story issues.
Spinning items lagged the game from 50 fps to 20
Videos didn't play until i ran: "protontricks 477740 lavfilters"