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Season One
1. Pilot
2. Deep Throat
3. Squeeze
4. Conduit
5. The Jersey Devil
6. Shadows
7. Ghost in the Machine
8. Ice
9. Space
10. Fallen Angel
11. Eve
12. Fire
13. Beyond the Sea
14. Genderbender
15. Lazarus
16. Young at Heart
17. E.B.E.
18. Miracle Man
19. Shapes
20. Darkness Falls
21. Tooms
22. Born Again
23. Roland
24. The Erlenmeyer Flask
Season Two
25. Little Green Men
26. The Host
27. Blood
28. Sleepless
29. Duane Barry (1)
30. Ascension (2)
31. 3
32. One Breath
33. Firewalker
34. Red Museum
35. Excelsis Dei
36. Aubrey
37. Irresistible
38. Die Hand die Verletzt
39. Fresh Bones
40. Colony (1)
41. End Game (2)
42. Fearful Symmetry
43. Død Kalm
44. Humbug
45. The Calusari
46. F. Emasculata
47. Soft Light
48. Our Town
49. Anasazi (1)
Season Three
50. The Blessing Way (2)
51. Paper Clip (3)
52. D.P.O.
53. Clyde Bruckman’s Final Repose
54. The List
55. 2Shy
56. The Walk
57. Oubliette
58. Nisei (1)
59. 731 (2)
60. Revelations
61. War of the Coprophages
62. Syzygy
63. Grotesque
64. Piper Maru (1)
65. Apocrypha (2)
66. Pusher
67. Teso Dos Bichos
68. Hell Money
69. Jose Chung’s From Outer Space
70. Avatar
71. Quagmire
72. Wetwired
73. Talitha Cumi (1)
Season four
74. Herrenvolk (2)
75. Home
76. Teliko
77. Unruhe
78. The Field Where I Died
79. Sanguinarium
80. Musings of a Cigarette-Smoking Man
81. Tunguska (1)
82. Terma (2)
83. Paper Hearts
84. El Mundo Gira
85. Leonard Betts
86. Never Again
87. Memento Mori
88. Kaddish
89. Unrequited
90. Tempus Fugit (1)
91. Max (2)
92. Synchrony
93. Small Potatoes
94. Zero Sum
95. Elegy
96. Demons
97. Gethsemane (1)
Season five
98. Redux (2)
99. Redux II (3)
100. Unusual Suspects
101. Detour
102. The Post-Modern Prometheus
103. Christmas Carol (1)
104. Emily (2)
105. Kitsunegari
106. Schizogeny
107. Chinga
108. Kill Switch
109. Bad Blood
110. Patient X (1)
111. The Red and the Black (2)
112. Travelers
113. Mind’s Eye
114. All Souls
115. The Pine Bluff Variant
116. Folie a Deux
117. The End
Season six
118. The Beginning
119. Drive
120. Triangle
121. Dreamland (1)
122. Dreamland II (2)
123. How the Ghosts Stole Christmas
124. Terms of Endearment
125. The Rain King
126. S.R. 819
127. Tithonus
128. Two Fathers (1)
129. One Son (2)
130. Agua Mala
131. Monday
132. Arcadia
133. Alpha
134. Trevor
135. Milagro
136. The Unnatural
137. Three of a Kind
138. Field Trip
139. Biogenesis (1)
Season seven
140. The Sixth Extinction (2)
141. The Sixth Extinction II: Amor Fati (3)
142. Hungry
143. Millennium
144. Rush
145. The Goldberg Variation
146. Orison
147. The Amazing Maleeni
148. Signs and Wonders
149. Sein und Zeit (1)
150. Closure (2)
151. X-COPS
152. First Person Shooter
153. Theef
154. En Ami
155. Chimera
156. All Things
157. Brand X
158. Hollywood A.D.
159. Fight Club
160. Je Souhaite
161. Requiem
Season eight
162. Within (1)
163. Without (2)
164. Patience
165. Roadrunners
166. Invocation
167. Redrum
168. Via Negativa
169. Surekill
170. Salvage
171. Badlaa
172. The Gift
173. Medusa
174. Per Manum
175. This is Not Happening (1)
176. DeadAlive (2)
177. Three Words
178. Empedocles
179. Vienen
180. Alone
181. Essence (1)
182. Existence (2)
Season nine
183. Nothing Important Happened Today (1)
184. Nothing Important Happened Today II (2)
185. Dæmonicus
186. 4-D
187. Lord of the Flies
188. Trust No 1
189. John Doe
190. Hellbound
191. Provenance (1)
192. Providence (2)
193. Audrey Pauley
194. Underneath
195. Improbable
196. Scary Monsters
197. Jump the Shark
198. William
199. Release
200. Sunshine Days
201. The Truth (1)
202. The Truth (2)