| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Her Reason | 3 | 26 | Saturday April 3, 2004 |
| Teacher | 3 | 27 | Saturday April 10, 2004 |
| One is All, All is One | 3 | 28 | Saturday April 17, 2004 |
| Untainted Child | 3 | 29 | Saturday April 24, 2004 |
| South Headquarters Assault | 3 | 30 | Saturday May 1, 2004 |
| Sin | 3 | 31 | Saturday May 8, 2004 |
| Dante of the Deep Forest | 3 | 32 | Saturday May 15, 2004 |
| Al, Captured | 3 | 33 | Saturday May 29, 2004 |
| The Theory of Greed | 3 | 34 | Saturday June 5, 2004 |
| The Reunion of Fools | 3 | 35 | Saturday June 12, 2004 |
| The Sinner Within Me | 3 | 36 | Saturday June 19, 2004 |
| The Flame Alchemist/The Fighting Lieutenant/The Mystery of the 13th Warehouse | 3 | 37 | Saturday June 26, 2004 |
| With the River's Flow | 3 | 38 | Saturday July 3, 2004 |
| Eastern Civil War | 3 | 39 | Saturday July 10, 2004 |
| The Scar | 3 | 40 | Saturday July 17, 2004 |
| Holy Mother | 3 | 41 | Saturday July 24, 2004 |