Season 9
Aware his presence only puts Scully and William in jeopardy Mulder once again disappears — but at least this time it is his own choice. A frustrated Agent Doggett tries to find Mulder so he can proceed with his investigation against Deputy Director Kersh, but Scully and Skinner finally convince him to drop his case. Yet even as Scully helps Agent Doggett and Agent Reyes on some of their cases she realizes William is still in danger. When she learns a religious cult wants her son dead she turns to the Lone Gunmen. But even they cannot prevent William from being kidnapped, a fact which forces Scully to make a painful decision. Yet even in her darkest hour she receives word that Mulder has been found — and is being held in a military brig for the murder of a man who cannot die.
Episodes
1 Nothing Important Happened Today (1) Nov 11, 2001 
2 Nothing Important Happened Today II (2) Nov 18, 2001 
3 Dæmonicus Dec 2, 2001 
4 4-D Dec 9, 2001 
5 Lord of the Flies Dec 16, 2001 
6 Trust No 1 Jan 6, 2002 
7 John Doe Jan 13, 2002 
8 Hellbound Jan 27, 2002 
9 Provenance (1) Mar 3, 2002 
10 Providence (2) Mar 10, 2002 
11 Audrey Pauley Mar 17, 2002 
12 Underneath Mar 31, 2002 
13 Improbable Apr 7, 2002 
14 Scary Monsters Apr 14, 2002 
15 Jump the Shark Apr 21, 2002 
16 William Apr 28, 2002 
17 Release May 5, 2002 
18 Sunshine Days May 12, 2002 
19 The Truth (1) May 19, 2002 
20 The Truth (2) May 19, 2002