Metro 2033 was for me. Then I played the remaster and it seemed really obvious, so IDK if I was really oblivious back then, they made it more obvious in the remake, or my potato of a computer at the time made it really hard to notice
spoiler
the alien helping you survive all the anomalies that were killing everyone else.
Final Fantasy 3 (6 in Japan)
Castlevania:SOTN
Silent Hill 2
Metro 2033 was for me. Then I played the remaster and it seemed really obvious, so IDK if I was really oblivious back then, they made it more obvious in the remake, or my potato of a computer at the time made it really hard to notice
spoiler
the alien helping you survive all the anomalies that were killing everyone else.
Prey 2017 is worth mentioning