| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The Secret Mission | 2 | 35 | Friday April 5, 2002 |
| Sniper | 2 | 36 | Monday April 8, 2002 |
| The Blue Devil | 2 | 37 | Tuesday April 9, 2002 |
| The Steel Bison | 2 | 38 | Wednesday April 10, 2002 |
| The Invisible Enemy | 2 | 39 | Thursday April 11, 2002 |
| The Zoid Hunters | 2 | 40 | Friday April 12, 2002 |
| The Devil's Maze | 2 | 41 | Monday April 15, 2002 |
| Raven | 2 | 42 | Tuesday April 16, 2002 |
| The Emperor's Holiday | 2 | 43 | Wednesday April 17, 2002 |
| Assault of the Mega Monster | 2 | 44 | Thursday April 18, 2002 |
| The Wings of Darkness | 2 | 45 | Friday April 19, 2002 |
| The Devil of the Sea | 2 | 46 | Monday April 22, 2002 |
| A Monster Awakens | 2 | 47 | Tuesday April 23, 2002 |
| The Black Lightning | 2 | 48 | Wednesday April 24, 2002 |
| The Distant Stars | 2 | 49 | Thursday April 25, 2002 |
| Attack of the Geno Breaker (1) | 2 | 50 | Friday April 26, 2002 |
| The Boy from the Ruins (2) | 2 | 51 | Monday April 29, 2002 |
| Van's New Power | 2 | 52 | Tuesday April 30, 2002 |
| Phantom | 2 | 53 | Wednesday May 1, 2002 |
| G-File | 2 | 54 | Thursday May 2, 2002 |
| Supersonic Battle | 2 | 55 | Friday May 3, 2002 |
| Cerberus | 2 | 56 | Monday May 6, 2002 |
| The Nightmare | 2 | 57 | Tuesday May 7, 2002 |
| Attack of the Winged Dragons | 2 | 58 | Wednesday May 8, 2002 |
| The Capital Collapses | 2 | 59 | Thursday May 9, 2002 |
| The Giant Fortress | 2 | 60 | Monday May 13, 2002 |
| The Great Sea Battle | 2 | 61 | Tuesday May 14, 2002 |
| The Gravity Cannon | 2 | 62 | Wednesday May 15, 2002 |
| The Final Battle | 2 | 63 | Thursday May 16, 2002 |
| The Ancient Memory (1) | 2 | 64 | Saturday January 4, 2003 |
| Zoid Eve (2) | 2 | 65 | Saturday January 4, 2003 |
| Endgame (3) | 2 | 66 | Saturday January 4, 2003 |
| Return to Tomorrow (4) | 2 | 67 | Saturday January 4, 2003 |