Something that's done is finished, through, or over — it's no longer happening. If your final research paper is done, you've completed it.
You might announce at your high school graduation that you're done with school, or listen to your sister practicing the drums and hope she'll be done before bedtime. When food is described as done it means "ready to eat" or "thoroughly cooked." Many Thanksgiving feasts have to wait until the turkey is done. If you're "done for" in a video game, you're just about to die — your fate is sealed.