- Anywhere but Their Lips: Mulder kisses Scully's cheek in the car, while she's sleeping.
- Courtroom Episode
- The End of the World as We Know It: Revealed to be 22nd December, 2012, the end of the Mayan calendar by CSM.
- Heel–Face Turn: Kersh joins the good side.
- Joker Jury
- Killed Off for Real: Finally, Knowle Rohrer bites it courtesy the Anasazi ruins. Also, CSM. But ultimately subverted in Season 10.
- Not Quite Dead: CSM is revealed to be alive and hiding in the Anasazi ruins.