The Might&Magic games.

Septerra Core, maybe?

It's a good idea, I thought of it, which of them would happen to be the most sci-fantasy ? I know after 9 there are just Fantasy because it's not the same world...

Rudra no Hihou has a similar backstory to what you're thinking of. So does La Mulana.

As for Science Fantasy, here are some possibilities:
* Phantasy Star series
* Paladin's Quest and Lennus 2
* SaGa Frontier (arguably SaGa 1-3, though maybe not to the same extent)
* Any Star Wars game
* Centauri Alliance (note: Game is only for 8-bit computers and has some rough edges)
* Much of the Final Fantasy series
* Hoshi wo Miru Hito (WARNING: Game is not good; it's considered kusoge, and is comparable in quality to the likes of ET, Superman 64, Arabian Nights (PC, not Amiga) Ultima 5 NES, and Big Rigs. In other words, this is not a game you should strive to imitate, and it may be better to watch a speedrun rather than actually playing it.)

Edit: If you play SaGa Frontier, T260's scenario is probably closest to what you're looking for, though you could also try Red or Riki. Just don't do Lute's scenario first.

Arcanum: https://www.gog.com/game/arcanum_of_steamworks_and_magick_obscura

SEVEN: The Days Long Gone

One of the settings I've liked most.

^This was the game I was digging for in my mind and couldn't come up with when I read Numenera. :-)

Also, Wizardry 6-8 are good examples, especially Wizardry 8 with its gadgeteer class giving the player access to some strange high technology.

Also:

The Technomancer
Final Liberation
Warhammer 40,000: Chaos Gate
Warhammer 40,000: Rites of War
Warhammer 40,000: Fire Warrior
Warhammer 40,000: Armageddon
Battlefleet Gothic: Armada
Battlefleet Gothic: Armada II
Space Hulk: Deathwing
Warhammer 40,000: Sanctus Reach
Warhammer 40,000: Gladius - Relics of War
Warhammer 40,000: Mechanicus

Anachronox may also fit.

6 and 7.
They are all mostly Fantasy, though, with some SF elements mostly in the end game. And the overall story arc is more SF than Fantasy.

Tower of Time

It starts as generic fantasy, then become more steampunk-ish, and full sci-fi near the end.

Not a lot of sci-fi RPGs in general, let alone isometric ones. Numenera (which I haven't played yet) is a rare breed in that sense. Stasis probably would fit to some degree, as would Underrail, but neither perfectly.

As for sci-fi games in general, the Deus Ex series is an obvious one. Plus Prey and System Shock 2. These games are in my favorite genre: first-person RPG/FPS hybrids. Can't recommend them enough. Knights of the Old Republic is a good choice if you don't mind how very limited the gameplay is due to the Xbox. Dead Space is a great survival horror sci-fi series.

The Outer Worlds is only on Epic's store, but it is DRM free and a good little sci-fi Fallout clone (though more limited in scope and budget).