Out of jealousy, Keith was later murdered by Dan, right before Karen finds out she's pregnant with their daughter, Lily Roe Scott. Keith was seen in later episodes as a spirit watching over his loved ones.

Why did they kill off Keith?

In season three, Dan shot and killed Keith as he believed Keith had attempted to murder him in the dealership fire. After he was killed by Dan, Karen finds out that she is pregnant with his daughter Lilly Roe Scott.

Do they ever find out Dan killed Keith?

However, Hope returned and intervened before Lucas could ask her anything more. ... Having been threatened by Dan, Hope decided to move her and Abby away from Tree Hill for good but Abby couldn't leave without telling Lucas the truth and went to his house. She revealed that Dan Scott killed Keith ("The Runaway Found").