As your ship takes damage in battle, there is a chance that your crew will be injured aboard as sparks fly, fires flare up and things get blown to bits. Especially when your shields are down. And if the Life Support system is offline… yikes. In the HUD, you can get a sense of the danger your crew is in by how red their portraits get. The redder, the deader.
You, the captain, have a much higher tolerance for the destruction happening around you. Call it “plot armor” if you want, but I call it skill.
Eventually, your crew will be vanquished. You may feel sad for them. You may even say a few words for them. But fret not. Once you limp your ship back to a friendly station, you’ll find there are usually some people willing to join your crew.
And thus the cycle continues. You ramp up a new crew, stock up on supplies, maybe find a mission to do, and press on.