| Episode # | Prod # | Original Air Date | Episode Title | ||
| 0. | 0-1 | Fear Burns into Ashes | |||
| Season One | |||||
| 1. | 1-1 | 103 | 02-Oct-2000 | Under the Night (1) | |
| 2. | 1-2 | 104 | 09-Oct-2000 | An Affirming Flame (2) | |
| 3. | 1-3 | 102 | 16-Oct-2000 | To Loose the Fateful Lightning | |
| 4. | 1-4 | 101 | 23-Oct-2000 | D Minus Zero | |
| 5. | 1-5 | 106 | 30-Oct-2000 | Double Helix | |
| 6. | 1-6 | 108 | 06-Nov-2000 | Angel Dark, Demon Bright | |
| 7. | 1-7 | 107 | 13-Nov-2000 | The Ties That Blind | |
| 8. | 1-8 | 109 | 20-Nov-2000 | The Banks of the Lethe | |
| 9. | 1-9 | 105 | 27-Nov-2000 | A Rose in the Ashes | |
| 10. | 1-10 | 110 | 15-Jan-2001 | All Great Neptune's Ocean | |
| 11. | 1-11 | 111 | 22-Jan-2001 | The Pearls that Were His Eyes | |
| 12. | 1-12 | 112 | 29-Jan-2001 | The Mathematics of Tears | |
| 13. | 1-13 | 115 | 05-Feb-2001 | Music of a Distant Drum | |
| 14. | 1-14 | 113 | 12-Feb-2001 | Harper 2.0 | |
| 15. | 1-15 | 114 | 19-Feb-2001 | Forced Perspective | |
| 16. | 1-16 | 118 | 26-Feb-2001 | The Sum of Its Parts | |
| 17. | 1-17 | 120 | 09-Apr-2001 | Fear and Loathing in the Milky Way | |
| 18. | 1-18 | 116 | 16-Apr-2001 | The Devil Take the Hindmost | |
| 19. | 1-19 | 121 | 23-Apr-2001 | The Honey Offering | |
| 20. | 1-20 | 117 | 30-Apr-2001 | Star-Crossed | |
| 21. | 1-21 | 119 | 07-May-2001 | It Makes a Lovely Light | |
| 22. | 1-22 | 122 | 14-May-2001 | ... Its Hour Come Round at Last (1) | |
| Season Two | |||||
| 23. | 2-1 | 201 | 01-Oct-2001 | The Widening Gyre (2) | |
| 24. | 2-2 | 202 | 08-Oct-2001 | Exit Strategies | |
| 25. | 2-3 | 203 | 15-Oct-2001 | A Heart for Falsehood Framed | |
| 26. | 2-4 | 209 | 22-Oct-2001 | Pitiless as the Sun | |
| 27. | 2-5 | 206 | 29-Oct-2001 | Last Call at the Broken Hammer | |
| 28. | 2-6 | 204 | 05-Nov-2001 | All Too Human | |
| 29. | 2-7 | 207 | 12-Nov-2001 | Una Salus Victus | |
| 30. | 2-8 | 205 | 19-Nov-2001 | Home Fires | |
| 31. | 2-9 | 208 | 26-Nov-2001 | Into the Labyrinth | |
| 32. | 2-10 | 210 | 19-Jan-2002 | The Prince | |
| 33. | 2-11 | 211 | 26-Jan-2002 | Bunker Hill | |
| 34. | 2-12 | 212 | 02-Feb-2002 | Ouroborous | |
| 35. | 2-13 | 213 | 09-Feb-2002 | Lava and Rockets | |
| 36. | 2-14 | 216 | 16-Feb-2002 | Be All My Sins Remembered | |
| 37. | 2-15 | 214 | 23-Feb-2002 | Dance of the Mayflies | |
| 38. | 2-16 | 215 | 02-Mar-2002 | In Heaven Now Are Three | |
| 39. | 2-17 | 221 | 13-Apr-2002 | The Things We Cannot Change | |
| 40. | 2-18 | 217 | 20-Apr-2002 | The Fair Unknown | |
| 41. | 2-19 | 219 | 27-Apr-2002 | Belly of the Beast | |
| 42. | 2-20 | 218 | 04-May-2002 | The Knight, Death, and the Devil | |
| 43. | 2-21 | 220 | 11-May-2002 | Immaculate Perception | |
| 44. | 2-22 | 222 | 18-May-2002 | The Tunnel at the End of the Light | |
| Season Three | |||||
| 45. | 3-1 | 301 | 21-Sep-2002 | If the Wheel Is Fixed | |
| 46. | 3-2 | 302 | 28-Sep-2002 | The Shards of Rimni | |
| 47. | 3-3 | 303 | 05-Oct-2002 | Mad to Be Saved | |
| 48. | 3-4 | 304 | 11-Oct-2002 | Cui Bono | |
| 49. | 3-5 | 305 | 21-Oct-2002 | The Lone and Level Sands | |
| 50. | 3-6 | 306 | 28-Oct-2002 | Slipfighter the Dogs of War | |
| 51. | 3-7 | 307 | 11-Nov-2002 | The Leper's Kiss | |
| 52. | 3-8 | 308 | 18-Nov-2002 | For Whom the Bell Tolls | |
| 53. | 3-9 | 309 | 25-Nov-2002 | And Your Heart Will Fly Away... | |
| 54. | 3-10 | 310 | 20-Jan-2003 | The Unconquerable Man | |
| 55. | 3-11 | 311 | 27-Jan-2003 | Delenda Est | |
| 56. | 3-12 | 312 | 03-Feb-2003 | The Dark Backward | |
| 57. | 3-13 | 313 | 10-Feb-2003 | The Risk All Point | |
| 58. | 3-14 | 314 | 17-Feb-2003 | The Right Horse | |
| 59. | 3-15 | 315 | 24-Feb-2003 | What Happens to a Rev Deferred? | |
| 60. | 3-16 | 316 | 31-Mar-2003 | Point of the Spear | |
| 61. | 3-17 | 317 | 07-Apr-2003 | Vault of the Heavens | |
| 62. | 3-18 | 318 | 14-Apr-2003 | Deep Midnight's Voice | |
| 63. | 3-19 | 319 | 21-Apr-2003 | The Illusion of Majesty | |
| 64. | 3-20 | 320 | 28-Apr-2003 | Twilight of the Idols | |
| 65. | 3-21 | 321 | 05-May-2003 | Day of Judgement, Day of Wrath | |
| 66. | 3-22 | 322 | 12-May-2003 | Shadows Cast by a Final Salute | |
| Season Four | |||||
| 67. | 4-1 | 401 | 29-Sep-2003 | Answers Given to Questions Never Asked | |
| 68. | 4-2 | 402 | 06-Oct-2003 | Pieces of Eight | |
| 69. | 4-3 | 403 | 13-Oct-2003 | Waking the Tyrant's Device | |
| 70. | 4-4 | 404 | 20-Oct-2003 | Double or Nothingness | |
| 71. | 4-5 | 405 | 27-Oct-2003 | Harper/Delete | |
| 72. | 4-6 | 406 | 03-Nov-2003 | Soon the Nearing Vortex (1) | |
| 73. | 4-7 | 407 | 10-Nov-2003 | The World Turns All Around Her (2) | |
| 74. | 4-8 | 408 | 17-Nov-2003 | Conduit to Destiny | |
| 75. | 4-9 | 409 | 12-Jan-2004 | Machinery of the Mind | |
| 76. | 4-10 | 410 | 19-Jan-2004 | Exalted Reason, Resplendent Daughter | |
| 77. | 4-11 | 411 | 26-Jan-2004 | The Torment, The Release | |
| 78. | 4-12 | 412 | 02-Feb-2004 | The Spider's Stratagem | |
| 79. | 4-13 | 413 | 09-Feb-2004 | The Warmth of an Invisible Light | |
| 80. | 4-14 | 414 | 16-Feb-2004 | The Others | |
| 81. | 4-15 | 415 | 23-Feb-2004 | Fear Burns Down to Ashes | |
| 82. | 4-16 | 416 | 05-Apr-2004 | Lost in a Space that isn't There | |
| 83. | 4-17 | 417 | 12-Apr-2004 | Abridging the Devil's Divide | |
| 84. | 4-18 | 418 | 19-Apr-2004 | Trusting the Gordian Maze | |
| 85. | 4-19 | 419 | 26-Apr-2004 | A Symmetry of Imperfection | |
| 86. | 4-20 | 420 | 03-May-2004 | Time Out of Mind | |
| 87. | 4-21 | 421 | 10-May-2004 | The Dissonant Interval (1) | |
| 88. | 4-22 | 422 | 17-May-2004 | The Dissonant Interval (2) | |
| Season Five | |||||
| 89. | 5-1 | 501 | 24-Sep-2004 | The Weight (1) | |
| 90. | 5-2 | 502 | 01-Oct-2004 | The Weight (2) | |
| 91. | 5-3 | 503 | 08-Oct-2004 | Phear Phactor Phenom | |
| 92. | 5-4 | 504 | 15-Oct-2004 | Decay of the Angel | |
| 93. | 5-5 | 505 | 22-Oct-2004 | The Eschatology of Our Present | |
| 94. | 5-6 | 506 | 29-Oct-2004 | When Goes Around... | |
| 95. | 5-7 | 507 | 05-Nov-2004 | Attempting Screed | |
| 96. | 5-8 | 508 | 12-Nov-2004 | So Burn the Untamed Lands | |
| 97. | 5-9 | 509 | 19-Nov-2004 | What Will Be Was Not | |
| 98. | 5-10 | 510 | 07-Jan-2005 | The Test | |
| 99. | 5-11 | 511 | 14-Jan-2005 | Through A Glass Darkly | |
| 100. | 5-12 | 512 | 21-Jan-2005 | Pride Before The Fall | |
| 101. | 5-13 | 513 | 28-Jan-2005 | Moonlight Becomes You | |
| 102. | 5-14 | 514 | 04-Feb-2005 | Past Is Prolix | |
| 103. | 5-15 | 515 | 11-Feb-2005 | The Opposites Of Attraction | |
| 104. | 5-16 | 516 | 18-Feb-2005 | Saving Light From A Black Sun | |
| 105. | 5-17 | 517 | 08-Apr-2005 | Totaled Recall | |
| 106. | 5-18 | 518 | 15-Apr-2005 | Quantum Tractate Delirium | |
| 107. | 5-19 | 519 | 22-Apr-2005 | One More Day's Light | |
| 108. | 5-20 | 520 | 29-Apr-2005 | Chaos and the Stillness of It | |
| 109. | 5-21 | 521 | 06-May-2005 | The Heart of the Journey (1) | |
| 110. | 5-22 | 522 | 13-May-2005 | The Heart of the Journey (2) | |