| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Farewell Jaden! A Tearful Graduation Ceremony! | 4 | 179 | |
| 155 | 3 | 155 | |
| A Dimensional Duel | 3 | 128 | Saturday January 26, 2008 |
| A Duel In Love | 1 | 3 | Wednesday October 12, 2005 |
| A Greater Porpoise | 2 | 62 | Friday September 1, 2006 |
| A Hassleberry Hounding | 2 | 55 | Wednesday August 23, 2006 |
| A Looming Threat! The Mysterious Visitor! | 4 | 157 | |
| A Lying Legend | 1 | 40 | Tuesday February 28, 2006 |
| A New Breed of Hero (1) | 2 | 58 | Monday August 28, 2006 |
| A New Breed of Hero (2) | 2 | 59 | Tuesday August 29, 2006 |
| A New World Order | 3 | 132 | Saturday February 23, 2008 |
| A Reason to Win | 1 | 41 | Wednesday March 1, 2006 |
| A Sight Unseen (1) | 3 | 139 | Saturday April 12, 2008 |
| A Sight Unseen (2) | 3 | 140 | Saturday April 19, 2008 |
| A Snake in the Grass (1) | 3 | 117 | Saturday September 1, 2007 |
| A Snake in the Grass (2) | 3 | 118 | Saturday September 8, 2007 |
| A Snake in the Grass (3) | 3 | 119 | Saturday September 15, 2007 |
| A Spirit Summoned | 1 | 14 | Friday October 28, 2005 |
| Activate Super Fusion! Rainbow Neos | 3 | 152 | |
| Activate, Clear World! Ferocious Negative Effect! | 4 | 174 | |
| All For One! | 3 | 131 | Saturday February 16, 2008 |
| Amnael's Endgame (1) | 1 | 45 | Tuesday March 28, 2006 |
| Amnael's Endgame (2) | 1 | 46 | Wednesday March 29, 2006 |
| Armed Dragon VS Dragoon D End | 4 | 166 |
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