Let's be a bit more specific here: The first scene where the player encounters the marines is one where a scientist runs up to one of them, and gets gunned down by the marine.

That kind of scripted event, and environmental story-telling, was extremely novel in a FPS game back then.

It's easy to nowadays handwave that away as merely "Marines shoot player, player realizes Marines are enemy" like that kind of heavy scripting is just something mundane. But back then it wasn't mundane, it was quite revolutionary.

Before that the norm in the genre was mostly maze shooters with very limited NPC interactions, like certain Doom enemies fighting each other or some wall or another blowing up in Quake, Half-Life took all of that and brought it to a whole new level.