| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Electronic Money Panic | 2 | 32 | Saturday June 26, 2004 |
| Evil Empress Roll! (1) | 1 | 18 | Saturday May 1, 2004 |
| Evil Empress Roll! (2) | 1 | 19 | Monday May 3, 2004 |
| From Here To Revolutionary PET's | 2 | 51 | Thursday December 9, 2004 |
| Game Off! | 1 | 7 | Thursday November 25, 2004 |
| Get Dr. Regal! | 3 | 94 | Monday December 5, 2005 |
| Grave | 2 | 46 | Saturday July 31, 2004 |
| Guess Who's Coming To NetBattle? | 2 | 37 | Thursday December 2, 2004 |
| Hot Tempers! | 1 | 8 | Monday November 29, 2004 |
| Ice Ice Baby! | 1 | 6 | Wednesday November 24, 2004 |
| It's All How You Look at It! | 3 | 68 | Monday June 6, 2005 |
| Jack-In MegaMan! | 1 | 1 | Saturday May 17, 2003 |
| KnightMan's Betrayal! | 2 | 41 | Saturday July 3, 2004 |
| Magma Battle | 3 | 76 | Saturday June 18, 2005 |
| MegaMan Lives! | 1 | 25 | Saturday May 8, 2004 |
| Megaman Stolen | 2 | 26 | Friday October 15, 2004 |
| Metal Hot Spring! Ow It's Hot! | 3 | 57 | Friday March 4, 2005 |
| MistMan's Tower | 3 | 92 | Thursday December 1, 2005 |
| Mr. Wily's Legacy | 2 | 43 | Saturday July 17, 2004 |
| Ms. Yuri's Mission | 3 | 95 | Tuesday December 6, 2005 |
| N1 Grand Prix! | 1 | 10 | Saturday June 28, 2003 |
| Nebula's Great Invasion! | 3 | 87 | Saturday August 20, 2005 |
| Nebula's Secret Base | 3 | 79 | Saturday July 9, 2005 |
| NetCity No More! | 3 | 54 | Tuesday March 1, 2005 |
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