You wake up alone on a spaceship/station. Something has obviously gone wrong but you don't know what. As you explore, receiving instructions from someone who doesn't know much more than you do, you come across text messages that reveal a backstory involving a hostile AI being responsible for wiping out most of the crew and turning some of them into mindless cyborgs. Speaking of cyborgs, you also find some neat cybernetic enhancements along the way...

Yeah, okay, both games have the same premise.

Both had better engines than Doom - Marathon's engine was similar to the Jedi and Build engines in terms of supporting things like rooms over rooms (as long as you couldn't see both rooms at the same time), while System Shock's engine was a bit more quirky, being "true" 3D like Quake but still using 2D sprites and wanting everything to snap to an orthogonal grid like Wolfenstein or ROTT.

Both gave you an extremely clear idea of where you were going, what you were doing, and why, at a time when most first-person shooters boiled down to "find the level exit and whack it"

Both had health-recharging stations instead of traditional health powerups.

But here's the difference: System Shock's interface was poorly-thought-out, unplayable garbage, significantly worse than the dominant "arrow keys to move, alt/ctrl/spacebar to fire" control scheme of the day, whereas Marathon offered WASD + mouselook, which was significantly better. And this was in December of 1994, 1.5 years before Quake 1 would make mouselook available by typing some obscure commands into the console, 3 years before Quake II made it an option in the settings menu, and 5 years before Quake III and Unreal Tournament made it the default control scheme. Marathon also let the player carry whatever they could find rather than bogging the player down in a tedious inventory management system, and introduced alternate firing modes like Blood and Unreal would have years later instead of System Shock's tedious and clunky switching between ammunition types.

Back in 1994, PC gamers were obsessed with Doom and Doom II...

...nowadays, we say System Shock was the best FPS of 1994...

...but Mac users knew the truth all along, and we didn't believe them.