| episode | air date | countdown | title |
| S05E13 | 2013-01-18 | | An Enemy of Fate | |
| S05E12 | 2013-01-18 | | Liberty | |
| S05E11 | 2013-01-11 | | The Boy Must Live | |
| S05E10 | 2012-12-21 | | Anomaly XB-6783746 | |
| S05E09 | 2012-12-14 | | Black Blotter | |
| S05E08 | 2012-12-07 | | The Human Kind | |
| S05E07 | 2012-11-16 | | Five-Twenty-Ten | |
| S05E06 | 2012-11-09 | | Through the Looking Glass and What Walter Foun | |
| S05E05 | 2012-11-02 | | An Origin Story | |
| S05E04 | 2012-10-26 | | The Bullet That Saved The World | |
| S05E03 | 2012-10-12 | | The Recordist | |
| S05E02 | 2012-10-05 | | In Absentia | |
| S05E01 | 2012-09-28 | | Transilience Thought Unifier Model-11 | |
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| S04E22 | 2012-05-11 | | Brave New World (2) | |
| S04E21 | 2012-05-04 | | Brave New World (1) | |
| S04E20 | 2012-04-27 | | Worlds Apart | |
| S04E19 | 2012-04-20 | | Letters of Transit | |
| S04E18 | 2012-04-13 | | The Consultant | |
| S04E17 | 2012-04-06 | | Everything In Its Right Place | |
| S04E16 | 2012-03-30 | | Nothing as It Seems | |
| S04E15 | 2012-03-23 | | A Short Story About Love | |
| S04E14 | 2012-02-24 | | The End of All Things | |
| S04E13 | 2012-02-17 | | A Better Human Being | |
| S04E12 | 2012-02-10 | | Welcome to Westfield | |
| S04E11 | 2012-02-03 | | Making Angels | |
| S04E10 | 2012-01-27 | | Forced Perspective | |
| S04E09 | 2012-01-20 | | Enemy of My Enemy | |
| S04E08 | 2012-01-13 | | Back to Where You've Never Been | |
| S04E07 | 2011-11-18 | | Wallflower | |
| S04E06 | 2011-11-11 | | And Those We've Left Behind | |
| S04E05 | 2011-11-04 | | Novation | |
| S04E04 | 2011-10-14 | | Subject 9 | |
| S04E03 | 2011-10-07 | | Alone in the World | |
| S04E02 | 2011-09-30 | | One Night in October | |
| S04E01 | 2011-09-23 | | Neither Here Nor There | |
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| |
| S03E22 | 2011-05-06 | | The Day We Died | |
| S03E21 | 2011-04-29 | | The Last Sam Weiss | |
| S03E20 | 2011-04-22 | | 6:02 AM EST | |
| S03E19 | 2011-04-15 | | Lysergic Acid Diethylamide | |
| S03E18 | 2011-03-25 | | Bloodline | |
| S03E17 | 2011-03-18 | | Stowaway | |
| S03E16 | 2011-03-11 | | Os | |
| S03E15 | 2011-02-25 | | Subject 13 | |
| S03E14 | 2011-02-18 | | 6B | |
| S03E13 | 2011-02-11 | | Immortality | |
| S03E12 | 2011-02-04 | | Concentrate and Ask Again | |
| S03E11 | 2011-01-28 | | Reciprocity | |
| S03E10 | 2011-01-21 | | The Firefly | |
| S03E09 | 2010-12-09 | | Marionette | |
| S03E08 | 2010-12-02 | | Entrada | |
| S03E07 | 2010-11-18 | | The Abducted | |
| S03E06 | 2010-11-11 | | 6955 kHz | |
| S03E05 | 2010-11-04 | | Amber 31422 | |
| S03E04 | 2010-10-14 | | Do Shapeshifters Dream of Electric Sheep? | |
| S03E03 | 2010-10-07 | | The Plateau | |
| S03E02 | 2010-09-30 | | The Box | |
| S03E01 | 2010-09-23 | | Olivia | |
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| S02E23 | 2010-05-20 | | Over There, Part 2 | |
| S02E22 | 2010-05-13 | | Over There, Part 1 | |
| S02E21 | 2010-05-06 | | Northwest Passage | |
| S02E20 | 2010-04-29 | | Brown Betty | |
| S02E19 | 2010-04-22 | | The Man from the Other Side | |
| S02E18 | 2010-04-15 | | White Tulip | |
| S02E17 | 2010-04-08 | | Olivia. In The Lab. With The Revolver. | |
| S02E16 | 2010-04-01 | | Peter | |
| S02E15 | 2010-02-04 | | Jacksonville | |
| S02E14 | 2010-01-28 | | The Bishop Revival | |
| S02E13 | 2010-01-21 | | What Lies Below | |
| S02E12 | 2010-01-14 | | Johari Window | |
| S02E11 | 2010-01-11 | | Unearthed | |
| S02E10 | 2009-12-10 | | Grey Matters | |
| S02E09 | 2009-12-03 | | Snakehead | |
| S02E08 | 2009-11-19 | | August | |
| S02E07 | 2009-11-12 | | Of Human Action | |
| S02E06 | 2009-11-05 | | Earthling | |
| S02E05 | 2009-10-15 | | Dream Logic | |
| S02E04 | 2009-10-08 | | Momentum Deferred | |
| S02E03 | 2009-10-01 | | Fracture | |
| S02E02 | 2009-09-24 | | Night of Desirable Objects | |
| S02E01 | 2009-09-17 | | A New Day in the Old Town | |
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| S01E20 | 2009-05-12 | | There's More Than One of Everything | |
| S01E19 | 2009-05-05 | | The Road Not Taken | |
| S01E18 | 2009-04-28 | | Midnight | |
| S01E17 | 2009-04-21 | | Bad Dreams | |
| S01E16 | 2009-04-14 | | Unleashed | |
| S01E15 | 2009-04-07 | | Inner Child | |
| S01E14 | 2009-02-10 | | Ability | |
| S01E13 | 2009-02-03 | | The Transformation | |
| S01E12 | 2009-01-27 | | The No-Brainer | |
| S01E11 | 2009-01-20 | | Bound | |
| S01E10 | 2008-12-02 | | Safe | |
| S01E09 | 2008-11-25 | | The Dreamscape | |
| S01E08 | 2008-11-18 | | The Equation | |
| S01E07 | 2008-11-11 | | In Which We Meet Mr. Jones | |
| S01E06 | 2008-10-21 | | The Cure | |
| S01E05 | 2008-10-14 | | Power Hungry | |
| S01E04 | 2008-09-30 | | The Arrival | |
| S01E03 | 2008-09-23 | | The Ghost Network | |
| S01E02 | 2008-09-16 | | The Same Old Story | |
| S01E01 | 2008-09-09 | | Pilot | |
