The Booth and Bones exchange about Scully and Mulder mirrors an exchange with virtually the same lines from Pilot (2005).
While sifting through the remains at the Jeffersonian, Brennan and Wendell Bray have a conversation about going through the remains of a mass grave in Guatemala where she had to identify 500 victims and how horrible an experience it was. In Pilot (2005), Brennan had just returned from said mass grave in Guatemala.
This season has the least amount of episodes, only 12. The next shortest season is 7 with only 13 episodes.
Both of David Boreanaz parents are in this episode. His father Dave Roberts is the television anchor on the monitors reporting the explosion. His mother Pat Boreanaz hands Booth a folder at his office door.