Plot
Gordon informs Edward that Sir Topham Hatt, the director of the North Western Railway, has bought a new engine to arrange rolling stock in the shunting yard at Knapford. After helping Gordon up the hill with his goods train by pushing behind, Edward is shunting at Knapford Station when he overhears James talking to Thomas, Sir Topham Hatt's new tank engine. Gordon teases him about his size, but Sir Topham Hatt introduces himself and asks Edward to teach him how to work in the yard. Initially, Thomas grapples with a slow brake response and crossing into the others' train lines. He also cheekily whistles at Gordon one day while he is resting and wakes him up, much to Gordon's annoyance.
That stormy night at Tidmouth Sheds, Thomas meets Henry, whom Edward tells the story about the time he hid in a tunnel to get out of the rain, fearing it would ruin his green paint. The following day, Thomas is sent to the Sodor Steamworks where he is repainted blue and given the number NWR 1. After Gordon orders Thomas to fetch his express coaches, Thomas nearly takes two branch line coaches Annie and Clarabel, who belong to James, but take a swift liking to Thomas. Soon, seeing Henry at the water tower, Thomas asks him about his fear of the rain. Henry explains that the rain makes him nervous, but Thomas tries fruitlessly to convince him that there is nothing to be afraid of.
The following day, Thomas takes longer to start than usual and arrives late at Knapford with Gordon's coaches. Still cross with Thomas for waking him up, Gordon starts sooner than expected before Thomas can be uncoupled. By the time Gordon reaches Wellsworth, Thomas is worn out and uncoupled from the train. The next day, he accidentally disturbs two breakdown cranes named Judy and Jerome who are used for emergencies only.
The next morning, Henry falls ill and Thomas, being the only engine available, is instead asked to pull his train. Unfortunately, Thomas starts too soon and leaves the coaches behind, much to Sir Topham Hatt's dismay. Thomas sadly returns and is coupled to the train, but the other engines tease him about it at Tidmouth Sheds later that night. Edward kindly offers to let Thomas take his goods train for him the next day. However, Thomas brushes off Edward's advice about the Troublesome Trucks due to being too excited to take it, which leads him to almost have an accident after they push him down Gordon's Hill to the next station, where Sir Topham Hatt is waiting. Not approving of the engines' swap, he then orders Thomas and Edward to stay in the yard to fully educate Thomas about trucks. During this time, Thomas manages to help Henry overcome his fear of rain.
Sometime later, Thomas is working when a frightened James rushes by because the Troublesome Trucks have pushed him too much and his wooden brake blocks catch fire. Thomas chases after James and attempts to couple up behind him to stop him, but the trucks run James and themselves off the rails at a bend, which proves to Thomas that Edward was right about the trucks' foolishness. Thomas returns to Knapford and fetches Jerome and Judy to rescue James, who he takes to the Steamworks. Later that night, everyone congratulates Thomas and Sir Topham Hatt announces that James will be repaired and repainted, while Thomas will be rewarded with his own branch line. Everyone is happy for Thomas, except Gordon who asks who will fetch their coaches due to his belief that tender engines don't shunt. Sir Topham says the big engines will have to fetch their own coaches until he finds another small engine who can.
Later on, James returns to the yard, painted red with new brakes before Thomas is given Annie and Clarabel to run his branch line with. When arriving at Ffarquhar, he meets Glynn the "coffee-pot", who tells him to look after the branch line and wear his number with pride.
