| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Her Reason | 3 | 26 | Saturday May 7, 2005 |
| Teacher | 3 | 27 | Saturday September 17, 2005 |
| All is One, One is All | 3 | 28 | Saturday September 24, 2005 |
| The Untainted Child | 3 | 29 | Saturday October 1, 2005 |
| Assault on South Headquarters | 3 | 30 | Saturday October 8, 2005 |
| Sin | 3 | 31 | Saturday October 15, 2005 |
| Dante of the Deep Forest | 3 | 32 | Saturday October 22, 2005 |
| Al, Captured | 3 | 33 | Saturday October 29, 2005 |
| Theory of Avarice | 3 | 34 | Saturday November 5, 2005 |
| Reunion of the Fallen | 3 | 35 | Saturday November 12, 2005 |
| The Sinner Within | 3 | 36 | Saturday November 19, 2005 |
| The Flame Alchemist, The Bachelor Lieutenant, | 3 | 37 | Saturday November 26, 2005 |
| With the River's Flow | 3 | 38 | Saturday December 3, 2005 |
| Secret of Ishbal | 3 | 39 | Saturday December 10, 2005 |
| The Scar | 3 | 40 | Saturday December 17, 2005 |
| Holy Mother | 3 | 41 | Saturday January 7, 2006 |