The stories were a mix of those not shown in any episodes of Shining Time Station (mostly Season 4 episodes of Thomas the Tank Engine and Friends) and Season 3 episodes (such as Percy's Ghostly Trick). A music video was also included at the end of each episode.
- Missing Whistles - Mr. Conductor searches throughout Shining Time Station for his lost whistle.
- Wildlife - Mr. Conductor is accosted by wildlife as his tries to deliver a cookie to his tardy squirrel friends.
- Wish You Were Here - Unable to sleep, Mr. Conductor decides to write letters to his friends.
- For the Birds - Mr. Conductor tries to organize a benefit concert for the early birds when their nest was severely damaged during the previous night's wind storm.
- Splish, Splash, Splosh - Mr. Conductor is having a particularly bad day while going through his work. He realizes that this is the result of being impatient and remembers what happened to certain characters such as Duncan, Sir Handel and Peter Sam when they got impatient. Finally, he learns to calm down and not to be in a rush while learning the importance of patience.
- Paint the Town Red - Mr. Conductor tries various colors for his front door.
- Really Useful Engine (used in Missing Whistles)
- Toby (used in Wildlife)
- The Island Song (used in Wish You Were Here)
- Don't Judge a Book By Its Cover (used in For the Birds)
- Gone Fishing (used in Splish, Splash, Splosh)
- Let's Have A Race (used in Paint the Town Red)
- The opening credits and title cards of the episodes were similar to that of The Family Specials.
- The end credits consisted of deleted scenes from Season 3 of Thomas accompanied by the final stanza of Thomas' Anthem.
- While most Season 4 episodes of Thomas were new in this spin-off, the Thomas stories from One of the Family were repeated.