| Title | Season | Episode # | First Aired |
|---|---|---|---|
| XANA Awakens (1) | 3 | 53 | Monday October 2, 2006 |
| XANA Awakens (2) | 3 | 54 | Tuesday October 3, 2006 |
| Straight to Heart | 3 | 55 | Wednesday October 4, 2006 |
| Lyoko Minus One | 3 | 56 | Thursday October 5, 2006 |
| Tidal Wave | 3 | 57 | Friday October 6, 2006 |
| False Lead | 3 | 58 | Tuesday October 10, 2006 |
| Aelita | 3 | 59 | Wednesday October 11, 2006 |
| The Pretender | 3 | 60 | Thursday October 12, 2006 |
| The Secret | 3 | 61 | Friday October 13, 2006 |
| Temporary Insanity | 3 | 62 | Monday October 16, 2006 |
| Sabotage | 3 | 63 | Tuesday October 17, 2006 |
| Nobody in Particular | 3 | 64 | Wednesday October 18, 2006 |
| Triple Trouble | 3 | 65 | Thursday October 19, 2006 |
| Double Trouble | 3 | 66 | Friday October 20, 2006 |
| Final Round | 3 | 67 | Monday October 23, 2006 |