| Season One | Season Two | Season Three |
| Pilot | Little Green Men | The Blessing Way |
| Deep Throat | The Host | Paper Clip |
| Squeeze | Blood | D.P.O. |
| Conduit | Sleepless | Clyde Bruckman's Final Repose |
| The Jersey Devil | Duane Barry | The List |
| Shadows | Ascension | 2Shy |
| Ghost in the Machine | 3 | The Walk |
| Ice | One Breath | Oubliette |
| Space | Firewalker | Nisei |
| Fallen Angel | Red Museum | 731 |
| Eve | Excelsius Dei | Revelations |
| Fire | Aubrey | War of the Coprophages |
| Beyond the Sea | Irresistible | Syzygy |
| Genderbender | Die Hand Die Verletzt | Grotesque |
| Lazarus | Fresh Bones | Piper Maru |
| Young at Heart | Colony | Apocrypha |
| E.B.E. | End Game | Pusher |
| Miracle Man | Fearful Symmetry | Teso Dos Bichos |
| Shapes | Dod Kalm | Hell Money |
| Darkness Falls | Humbug | Jose Chung's "From Outer Space" |
| Tooms | The Calusari | Avatar |
| Born Again | F. Emasculata | Quagmire |
| Roland | Soft Light | Wetwired |
| The Erlenmeyer Flask | Our Town | Talitha Cumi |
| Anasazi |
| Season Four | Season Five |
| Herrenvolk | Unusual Suspects |
| Unruhe | Redux |
| Home | Redux II |
| Teliko | Detour |
| The Field Where I Died | Christmas Carol |
| Sanguinarium | Post-Modern Prometheus |
| Musings of a Cigarette Smoking Man | Emily |
| Paper Hearts | Kitsunegari |
| Tunguska | Schizogeny |
| Terma | Chinga |
| El Mundo Gira | Kill Switch |
| Kaddish | Bad Blood |
| Never Again | Patient "X" |
| Leonard Betts | The Red and the Black |
| Memento Mori | Travelers |
| Unrequited | Mind's Eye |
| Tempus Fugit | All Souls |
| Max | The Pine Bluff Variant |
| Synchrony | Folie a Deux |
| Small Potatoes | The End |
| Zero Sum | |
| Elegy | |
| Demons | |
| Gethsemane |
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