As soon as you'll realize that he's only the father of that daughter, Alyx Vance. He was in Black Mesa East before his arrest made it into the public. A few moments later, he was about to board a helicopter when a Combine Advisor killed him as he defended himself from this tentacle.

You then time travelled back to where he was and killed the Advisor, he said: "Gordon! Gordon! Wake up, Gordon! She's gone, Gordon. She's GONE."