Is MGS2: Substance not compressible?

I have tried following guides to compress/trim my ISO of Metal Gear Solid 2: Substance, but the and result appears to be a non-booting game. The ISO is generally around 6.5GB, yet it trims/compresses to about 2.3GB. There are about 2.3GB of files if you attempt to extract the ISO As well, but the game will no longer work once compressed like this, the uncompressed 6.5GB version of the ISO does.

Is there some hidden data or something on the ISO that breaks compression programs which does not appear as standard files? 6.5GB to 2.3GB is an insane level of compression, if the ISO was about 4.7GB or 8.5GB I would have assumed it was due to the rest of the disk being filled with dummy data like many Nintendo game disks are, but 6.5GB is rather specific, and it (supposedly) only containing 2.3GB of files is very suspicious. Especially when if I attempt to RAR the 6.5GB ISO (even with compression set high) I end up with a 4GB RAR file.
 
I have tried following guides to compress/trim my ISO of Metal Gear Solid 2: Substance, but the and result appears to be a non-booting game. The ISO is generally around 6.5GB, yet it trims/compresses to about 2.3GB. There are about 2.3GB of files if you attempt to extract the ISO As well, but the game will no longer work once compressed like this, the uncompressed 6.5GB version of the ISO does.

Is there some hidden data or something on the ISO that breaks compression programs which does not appear as standard files? 6.5GB to 2.3GB is an insane level of compression, if the ISO was about 4.7GB or 8.5GB I would have assumed it was due to the rest of the disk being filled with dummy data like many Nintendo game disks are, but 6.5GB is rather specific, and it (supposedly) only containing 2.3GB of files is very suspicious. Especially when if I attempt to RAR the 6.5GB ISO (even with compression set high) I end up with a 4GB RAR file.
MGS2 on PS2 is a dual layer game but each layer also contains different parts of the game, if you insert the disc and just look at the files you will only see the first layer, the 2nd layer is hidden, you would need something like the ps2 tool "apache" to see the 2nd layer, the game also needs to be rebuilt into that format too (or possibly patched to look into the same layer because the game expects certain files to be on the 2nd layer) so when you rebuild it make sure you make both layers and have the correct files on each layer.
 
Second layer is not hidden because it cannot be. Files however can be hidden in various of ways like eg. hidden and/or system attrib set on ISO9660 (eg. Tenchu: Stealth Assasins doing that, PSX game). Another way and this time not trivial is not writing specific file to fs, so it will not appear in tree view (eg. Final Fantasy 12 doing that and GT4 for second archive).

Super getting space compressing or files extracting smaller than image size doesn't mean that something is missing. If there are LBA gaps or dummy files, they will be efficiently compressed. However test with RAR was clever idea - it points that something indeed missing. If your ripping app rebuilding that image, it means it was not aware of data I mentioned in first two sentences above.

Rebuilding PS2 games is bad idea if you don't know what you doing. Many games using LBA order as security layer.
 
Second layer is not hidden because it cannot be. Files however can be hidden in various of ways like eg. hidden and/or system attrib set on ISO9660 (eg. Tenchu: Stealth Assasins doing that, PSX game). Another way and this time not trivial is not writing specific file to fs, so it will not appear in tree view (eg. Final Fantasy 12 doing that and GT4 for second archive).

Super getting space compressing or files extracting smaller than image size doesn't mean that something is missing. If there are LBA gaps or dummy files, they will be efficiently compressed. However test with RAR was clever idea - it points that something indeed missing. If your ripping app rebuilding that image, it means it was not aware of data I mentioned in first two sentences above.

Rebuilding PS2 games is bad idea if you don't know what you doing. Many games using LBA order as security layer.
MGS2 (and MGS3) has 2 layers to the games disc, each layer holds its own filelist, the files are NOT hidden attribute files, it actually has 2 lots of filesystem lists (so it each layer has a list of the files on it), which is why pretty much no program will display the correct files (so things like IsoBuster and 99% of all other ISO programs won't see it), each layer of the game is basically its own ISO (yes thats right each layer has its own headers), So each layer has its own Tree view but most programs only read the first so they only see layer1, layer2 isnt really hidden its just most programs dont know how to read it, i just said hidden because if you are using Windows Explorer or 99% of ISO extracting programs it will be hidden and you will only end up with the files in "layer1"
Not sure if this was unique to this game or not, i havent really looked that deeply into PS2 games but i remember when i did look into it like 15 years ago it was very strange, i hadnt seen another game like it.
And yeah i agree i really wouldn't recommend rebuilding it, the game does require files to be in the correct layer and possibly in the correct LBA position so its really not worth it.
 
tl;dr
PS2 Games on DL use TWO TOCs! One for each layer!
Thanks for Confirming that, wasnt sure if it was just MGS2+3 or if other games did it too.

Does it have 2nd list? TBH I not remember that but I will check and let know to the IsoBuster author.
That would be great, having a decent tool for it would be very handy to have it in there, previously i had to use the above mentioned cursed tool or split it in half and treat each layer as a seperate iso.

Use Apache3 by Sonix/Pix Creations to see the second layer.
Thanks i couldnt remember the exact name or version i just remembered it was Apache.

Apache 3 Preview is backdoor. Probably these servers are long dead now but still it is not wise to run it.
Oh i wasnt aware it was a backdoor, looking at it in virustotal those are some pretty sus addresses it tries to access, but they could also just be update servers (, its also packed with a custom version of upx which makes most virus scanners find it sus,
either way better not to use it anyway but it was the only tool that reads both layers so if you "have" to run it, make sure to use a sandbox environment (like sandboxie) and deny it internet access. At least until ISOBuster can get support added :)
 
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