Season One (2004-2005)
- 1 x 01 – Pilot: Part 1
- 1 x 02 – Pilot: Part 2
- 1 x 03 – Tabula Rasa
- 1 x 04 – Walkabout
- 1 x 05 – White Rabbit
- 1 x 06 – House of the Rising Sun
- 1 x 07 – The Moth
- 1 x 08 – Confidence Man
- 1 x 09 – Solitary
- 1 x 10 – Raised by Another
- 1 x 11 – All the Best Cowboys Have Daddy Issues
- 1 x 12 – Whatever the Case May Be
- 1 x 13 – Hearts and Minds
- 1 x 14 – Special
- 1 x 15 – Homecoming
- 1 x 16 – Outlaws
- 1 x 17 – …In Translation
- 1 x 18 – Numbers
- 1 x 19 – Deus Ex Machina
- 1 x 20 – Do No Harm
- 1 x 21 – The Greater Good
- 1 x 22 – Born to Run
- 1 x 23 – Exodus: Part 1
- 1 x 24/25 – Exodus: Part 2
Season Two (2005-2006)
- 2 x 01 – Man of Science, Man of Faith
- 2 x 02 – Adrift
- 2 x 03 – Orientation
- 2 x 04 – Everybody Hates Hugo
- 2 x 05 – …And Found
- 2 x 06 – Abandoned
- 2 x 07 – The Other 48 Days
- 2 x 08 – Collision
- 2 x 09 – What Kate Did
- 2 x 10 – The 23rd Psalm
- 2 x 11 – The Hunting Party
- 2 x 12 – Fire + Water
- 2 x 13 – The Long Con
- 2 x 14 – One of Them
- 2 x 15 – Maternity Leave
- 2 x 16 – The Whole Truth
- 2 x 17 – Lockdown
- 2 x 18 – Dave
- 2 x 19 – S.O.S.
- 2 x 20 – Two for the Road
- 2 x 21 – ?
- 2 x 22 – Three Minutes
- 2 x 23 – Live Together, Die Alone
Season Three (2006-2007)
- 3 x 01 – A Tale of Two Cities
- 3 x 02 – The Glass Ballerina
- 3 x 03 – Further Instructions
- 3 x 04 – Every Man for Himself
- 3 x 05 – The Cost of Living
- 3 x 06 – I Do
- 3 x 07 – Not in Portland
- 3 x 08 – Flashes Before Your Eyes
- 3 x 09 – Stranger in a Strange Land
- 3 x 10 – Tricia Tanaka is Dead
- 3 x 11 – Enter 77
- 3 x 12 – Par Avion
- 3 x 13 – The Man from Tallahassee
- 3 x 14 – Expose
- 3 x 15 – Left Behind
- 3 x 16 – One of Us
- 3 x 17 – Catch 22
- 3 x 18 – D.O.C.
- 3 x 19 – The Brig
- 3 x 20 – The Man Behind the Curtain
- 3 x 21 – Greatest Hits
- 3 x 22 – Through the Looking Glass
Season Four (2008)
- 4 x 01 – The Beginning of the End
- 4 x 02 – Confirmed Dead
- 4 x 03 – The Economist
- 4 x 04 – Eggtown
- 4 x 05 – The Constant
- 4 x 06 – The Other Woman
- 4 x 07 – Ji Yeon
- 4 x 08 – Meet Kevin Johnson
- 4 x 09 – The Shape of Things to Come
- 4 x 10 – Something Nice Back Home
- 4 x 11 – Cabin Fever
- 4 x 12 – There’s No Place Like Home: Part 1
- 4 x 13/14 – There’s No Place Like Home: Part 2
Season Five (2009)
- 5 x 01 – Because You Left
- 5 x 02 – The Lie
- 5 x 03 – Jughead
- 5 x 04 – The Little Prince
- 5 x 05 – This Place is Death
- 5 x 06 – 316
- 5 x 07 – The Life and Death of Jeremy Bentham
- 5 x 08 – LaFleur
- 5 x 09 – Namaste
- 5 x 10 – He’s Our You
- 5 x 11 – Whatever Happened, Happened
- 5 x 12 – Dead is Dead
- 5 x 13 – Some Like It Hoth
- 5 x 14 – The Variable
- 5 x 15 – Follow the Leader
- 5 x 16/17 – The Incident
Season Six (2010)
- 6 x 01/02 – LA X
- 6 x 03 – What Kate Does
- 6 x 04 – The Substitute
