Prey, System Shock 2, Outer Wilds, and Undertale are fully-realized microcosms where the primary game is unfolding the complex origami of the setting. All of them absolutely beautiful to experience.

Supergiant games' holy trinity: Bastion, Transistor and Pyre.

Also, the only Borderland games 1 and 2; don't believe the lies there are no more true Borderlands games and no there most certainly is no movie.

There's also one other, but you'll need a crowbar or a gravity gun in hand for me to tell you about it.

Clair Obscur: Expedition 33
Disco Elysium
Alpha Centauri
Super Marios Bros 3
Bloodborne
Ori 1 & 2
Fallout 1 & 2
Planescape: Torment
The Outer Wilds

Do you think Return of the Obra Dinn would belong alongside these or is that game too flawed by comparison? I ask because I myself am not sure.

Oh, actually Disco Elysium would fit right in here as well as a "fully-realized microcosms where the primary game is unfolding the complex origami of the setting".

Historically a masterpiece has been a (or the) work that demonstrates an artist is capable of utilizing their medium to its fullest extent, i.e. it has been mastered. Per ye olde Wiki:

Historically, a "masterpiece" was a work of a very high standard produced by an apprentice to obtain full membership, as a "master", of a guild or academy in various areas of the visual arts and crafts.

In that light, I'd say the best qualified would be games that completely utilized the capabilities of the platform they were designed for or, perhaps of interest to more people, expanded what everyone thought could be done with those systems. Games which were furthermore well polished and complete, and did not have much room for improvement taking into account the constraints they had to work with at the time. (For instance: No duh we could make Mario 64 run at a higher framerate and have better textures to look nicer on hardware now. That doesn't mean it wasn't arguably a masterpiece of its time, on the system it was on.) This doesn't just have to be technical stuff -- It could be the way the game used storytelling, its gameplay mechanics, or anything else.

Have you played Prey? Only other game to scratch that same itch for me.

Nioh 2 is one of my favorite soulslikes, but falls short of masterpiece in my opinion due to the repeatedly recycled levels.

RDR2. Witcher 3. Fallout New Vegas.

Fallout 2

Wasteland 3.

Curious to hear what the criteria for "masterpiece" is, otherwise I think it is just peoples' subjective opinion of what makes a great game that they also think others might agree about being a great game. Genuinely curious, interested in discussion, not saying this to shut down any of the answers here.

There are a lot of answers, mine will be drowned but... there it is. In no particular order :

• Final Fantasy X
• Clair Obscur : Expedition 33
• Baldur's Gate 3
• Kingdom Hearts 1 & 2 (but you had to be there when it came out)
• Metal Gear Solid 3
• Shadow Hearts : Covenant
• Kya : Dark Lineage (the bugs were a feature)
• Horizon : Zero Dawn
• Megaman (any megaman will do)
• Crash Bandicoot Trilogy
• Spyro Trilogy
• Pokemon Yellow/Crystal/Emerald
• Pokemon Jade (yes that bootleg version)
• The Last of Us (pt. I & II)
• Astroneer
• GTA : Vice City
• Unreal Tournament 2004
• CS 1.6 played in the most dirty lan at your disposal
• Control
• Tetris
• Neverwinter Nights 2
• Dragon Age : Origins
• Quake III
• Bomberman

My Picks...

Deus Ex (So many games try to be this and fail)

Cyberpunk (This one eventually measured up)

Alpha Centauri (Innovation mixed with familiarity and setting)

Fallout 2 (they're all good. Fallout 2 is special)

Kotor (Star Wars story telling in a beautiful way)

Baldur's Gate 2 and 3 (I'm stunned that 3 was a worthy successor)

Homeworld (One of the World's truly beautiful games)