Her he tells the whole truth, the cloning, the termination. Well... nearly the whole truth. He doesn't tell her Samantha was his sister. He's not quite sure why.

But he does destroy her former life, and his as well. She leaves behind her old identity to assume the one that the Gunmen created. He doesn't tell her the most important fact of all, who she really is to him. As a consequence, Fox Mulder, the man who spent his life searching for the truth, ends up living a lie. I want to cry, just thinking about it.