| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Tag Team Trial (1) | 1 | 10 | Monday October 24, 2005 |
| Tag Team Trial (2) | 1 | 11 | Tuesday October 25, 2005 |
| Taken By Storm (1) | 2 | 75 | Friday October 13, 2006 |
| Taken By Storm (2) | 2 | 76 | Monday October 16, 2006 |
| The Art of the Duel | 2 | 86 | Saturday January 6, 2007 |
| The Clash of Fate! Cyber-Style VS the Gem Beasts! | 3 | 147 | |
| The Combo of Terror! Nihility and Infinity! | 4 | 177 | |
| The Dark Light | 2 | 97 | Tuesday February 13, 2007 |
| The Dark Scorpions | 1 | 39 | Monday February 27, 2006 |
| The Darkness Is Revealed | 3 | 138 | Saturday April 5, 2008 |
| The Darkness Within | 2 | 89 | Wednesday January 31, 2007 |
| The Demon | 2 | 57 | Friday August 25, 2006 |
| The Duel Giant | 1 | 16 | Tuesday November 15, 2005 |
| The Duel Off (1) | 1 | 21 | Tuesday November 22, 2005 |
| The Duel Off (2) | 1 | 22 | Wednesday November 23, 2005 |
| The End of Destiny! Magma Neos VS Dark Ruler! | 4 | 171 | |
| The Fear Factor | 1 | 34 | Monday February 6, 2006 |
| The Forbidden Ritual (1) | 3 | 144 | Saturday May 17, 2008 |
| The Forbidden Ritual (2) | 3 | 145 | Saturday May 24, 2008 |
| The Graduation Duel Starts! Neos VS Horus the Black Flame Dragon | 4 | 168 | |
| The Hands of Justice (1) | 2 | 102 | Wednesday February 21, 2007 |
| The Hands of Justice (2) | 2 | 103 | Thursday February 22, 2007 |
| The Inherited Cyber Dark Dragon | 4 | 164 | |
| The Key Factor | 2 | 99 | Thursday February 15, 2007 |
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