SD in SD-6 stands for Section Disparu (the section that doesn't exist).
This episode didn't include Sydney's opening narration explaining the premise of the show, probably because during the course of her interrogation Sydney explained the show's setup.
Number 47: Haladki says that they have decoded 47 Rambaldi predictions.
Sydney breathing air from the tire is a nod to A View to a Kill (1985) in which Roger Moore played the leading role. Moore also guest starred as Edward Poole in The Prophecy (2002).