| Title | Season | Episode # | First Aired |
|---|---|---|---|
| CrossFusion | 3 | 53 | Monday November 22, 2004 |
| NetCity No More! | 3 | 54 | Tuesday March 1, 2005 |
| Bubble Trouble | 3 | 55 | Wednesday March 2, 2005 |
| DoubleSoul! | 3 | 56 | Thursday March 3, 2005 |
| Metal Hot Spring! Ow It's Hot! | 3 | 57 | Friday March 4, 2005 |
| A Dangerous Bowling Game | 3 | 58 | Monday March 7, 2005 |
| The CyberGarden Of Doom! | 3 | 59 | Tuesday March 8, 2005 |
| The Friendship In The Mirror | 3 | 60 | Wednesday March 9, 2005 |
| Dex Returns! | 3 | 61 | Thursday March 10, 2005 |
| Threat of the DarkChips | 3 | 62 | Monday March 14, 2005 |
| The Unsafe Safe | 3 | 63 | Tuesday March 15, 2005 |
| Code Of Conduct | 3 | 64 | Monday April 11, 2005 |
| CrossFusion For All! | 3 | 65 | Monday April 18, 2005 |
| The Purloined Princess | 3 | 66 | Thursday March 17, 2005 |
| The Incredible Guts! | 3 | 67 | Monday April 25, 2005 |
| It's All How You Look at It! | 3 | 68 | Monday June 6, 2005 |
| SavageMan Returns! | 3 | 69 | Monday May 2, 2005 |
| The Man From Sharo | 3 | 70 | Monday May 9, 2005 |
| Search Soul | 3 | 71 | Monday May 16, 2005 |
| Dark Secret | 3 | 72 | Monday May 23, 2005 |
| ShadeMan's Ambition | 3 | 73 | Monday May 30, 2005 |
| BubbleMan's Plan | 3 | 74 | Saturday September 10, 2005 |
| A Scary Power Of A Shiver | 3 | 75 | Monday June 13, 2005 |
| Magma Battle | 3 | 76 | Saturday June 18, 2005 |
| Videoman Returns | 3 | 77 | Saturday June 25, 2005 |
| Anetta's Revenge | 3 | 78 | Saturday July 2, 2005 |
| Nebula's Secret Base | 3 | 79 | Saturday July 9, 2005 |
| Wavering Heart | 3 | 80 | Saturday July 16, 2005 |
| Chaud vs. ProtoMan | 3 | 81 | Saturday July 23, 2005 |
| SpoutMan's New Hero | 3 | 82 | |
| Space Junk! | 3 | 83 | Saturday July 30, 2005 |
| Commander Beef Returns | 3 | 84 | Saturday September 3, 2005 |
| The BattleChip Gate! | 3 | 85 | Saturday August 6, 2005 |
| Wanted: Prisman! | 3 | 86 | Saturday August 13, 2005 |
| Nebula's Great Invasion! | 3 | 87 | Saturday August 20, 2005 |
| The New PET | 3 | 88 | Saturday August 27, 2005 |
| The Mysterious Masked Navi | 3 | 89 | Monday November 28, 2005 |
| Underground Hero | 3 | 90 | Tuesday November 29, 2005 |
| Allegro | 3 | 91 | Wednesday November 30, 2005 |
| MistMan's Tower | 3 | 92 | Thursday December 1, 2005 |
| The Great NetPolice Battle! | 3 | 93 | Friday December 2, 2005 |
| Get Dr. Regal! | 3 | 94 | Monday December 5, 2005 |
| Ms. Yuri's Mission | 3 | 95 | Tuesday December 6, 2005 |
| ProtoMan Returns | 3 | 96 | Wednesday December 7, 2005 |
| Dark vs. Dark | 3 | 97 | Thursday December 8, 2005 |
| Dr. Regal's Rampage | 3 | 98 | Friday December 9, 2005 |