Bones: Maybe, it wasn't a UFO that Cal saw. He could have seen something else.
Booth: (Sarcastically) Oh, yeah, like a Death Beam, or a Space Baby.
Bones: I was thinking more along the lines of spy satellite or experimental technology. You know, maybe the Agency was afraid Cal's sharing sensitive information with the STC.
Booth: Regardless, our government does not kill people, okay Bones?
Bones: (Scoffs) You were a sniper. Wasn't it our Government who sent you to kill people? (Booth looks at her a little hurt) Just saying.