Just curious, I usually like that about games.

If you kill (enough) civilians Citadel will send Ranger Team Delta to hunt you down. It's practically bad end as you can no longer complete the game or even level up as you do so by contacting citadel by radio.

You can piss of people by doing things they don't like or working for people they don't like. You can be quite an ass in the game but don't be surprised if people will be less welcoming or willing to help you out.

I don't remember game having any sort of general karma/morale/ethics system that is tracked thru whole game though. But it's been a while since I played.