| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Jacob Two-Two and the Boogie Beastie | 4 | 39 | Sunday January 1, 2006 |
| Jacob Two-Two and the Crumbling Cookie | 4 | 40 | Sunday January 1, 2006 |
| Jacob Two-Two and the Broadcast Bungle | 4 | 41 | Sunday January 1, 2006 |
| Jacob Two-Two and the Cranial Classroom Caper | 4 | 42 | Sunday January 1, 2006 |
| Jacob Two-Two and the Wicked Glitch | 4 | 43 | Sunday January 1, 2006 |
| Jacob Two-Two and the Big Brain Exchange | 4 | 44 | Sunday January 1, 2006 |
| Jacob Two-Two and the Teacher's Pet | 4 | 45 | Sunday January 1, 2006 |
| Jacob Two-Two and the Valentine's Day Disaster | 4 | 46 | Sunday January 1, 2006 |
| Jacob Two-Two and the Molecular Mayhem | 4 | 47 | Sunday February 12, 2006 |
| Jacob Two-Two and the Puzzling Portable | 4 | 48 | Monday February 13, 2006 |
| Jacob Two-Two and the Priceless Puck | 4 | 49 | Sunday January 1, 2006 |
| Jacob Two-Two and the Mata Hari Hamster | 4 | 50 | Sunday January 1, 2006 |
| Jacob Two-Two and the Halloween Hullabaloo | 4 | 51 | Sunday January 1, 2006 |
| Jacob Two-Two and the Wooden Nickel Knucklehead | 4 | 52 | Sunday January 1, 2006 |