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Looking for filler episodes? View the filler guide.
| # | Title | Aired | Type |
|---|---|---|---|
| 1 | 2315: Allied Forces Military Academy | Jan 3, 2004 | Canon |
| 2 | 2316: Field Training | Jan 10, 2004 | Canon |
| 3 | 1594: The Assassination of Totomi Hideyoshi | Jan 17, 2004 | Canon |
| 4 | 1594: Grotesque Shadow | Jan 24, 2004 | Canon |
| 5 | 1936: The 2-2-6 Incident | Jan 31, 2004 | Canon |
| 6 | 2305: Allied Military Naval Base | Feb 7, 2004 | Canon |
| 7 | The Two Watcher's Nests | Feb 14, 2004 | Canon |
| 8 | Soldiers Return | Feb 21, 2004 | Canon |
| 9 | The Ruin's Secret | Feb 28, 2004 | Canon |
| 10 | Hidden Past | Mar 6, 2004 | Canon |
| 11 | Overlapping Timelines | Mar 13, 2004 | Canon |
| 12 | Mission 4 | Mar 20, 2004 | Canon |
| 13 | Misaki | Mar 27, 2004 | Canon |