| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Playing with a Parasite (2) | 2 | 64 | Saturday February 22, 2003 |
| Pyramid of Light | 3 | 144 | Friday August 13, 2004 |
| Rage of the Egyptian Gods | 2 | 85 | Saturday September 20, 2003 |
| Reliving the Past | 4 | 164 | Saturday January 29, 2005 |
| Rise of the Great Beast (1) | 4 | 183 | Saturday May 28, 2005 |
| Rise of the Great Beast (2) | 4 | 184 | Saturday May 28, 2005 |
| Self Destruction | 4 | 163 | Saturday January 29, 2005 |
| Settling the Score (1) | 3 | 108 | Saturday December 13, 2003 |
| Settling the Score (2) | 3 | 109 | Saturday December 20, 2003 |
| Shadow of a Duel | 2 | 79 | Saturday August 16, 2003 |
| Shining Friendship | 1 | 25 | Saturday April 27, 2002 |
| Showdown in the Shadows (1) | 2 | 96 | Saturday October 25, 2003 |
| Showdown in the Shadows (2) | 2 | 97 | Saturday November 1, 2003 |
| Sinister Secrets (1) | 5 | 196 | Saturday October 1, 2005 |
| Sinister Secrets (2) | 5 | 197 | Saturday October 8, 2005 |
| Sinister Secrets (3) | 5 | 198 | Saturday October 8, 2005 |
| So Close Yet So Far | 3 | 119 | Saturday March 20, 2004 |
| Spiritual Awakening | 5 | 200 | Saturday October 22, 2005 |
| Stalked by the Rare Hunters | 2 | 55 | Saturday December 14, 2002 |
| Steppin' Out | 2 | 53 | Saturday November 23, 2002 |
| The Challenge | 4 | 155 | Saturday November 6, 2004 |
| The Creator Returns | 4 | 148 | Saturday October 2, 2004 |
| The Dark One Cometh (1) | 5 | 215 | Saturday April 8, 2006 |
| The Dark One Cometh (2) | 5 | 216 | Saturday April 15, 2006 |
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