It was part of the Gormagon story arc, which took place entirely in season 3. You should watch The Widow's Son in the Windshield, (maybe The Intern in the Incinerator if you want a few more details) The Knight on the Grid, and The Pain in the Heart for it all. If you don't want to watch those awesome episodes, I could explain it. :p

I started watching Bones during season 3 in the middle of the Gormagon story. I remember the Intern in the Incinerator episode. I will go find the other episodes. I'm sure I've seen most of the ones you mentioned but apparently not the one I need to see. Thanks for the episode titles I will need to find. :)