Thomas and the Polar Express is the third movie of Chuggington: Meet Thomas, Trainees!. It follows around Thomas having his adventure with "the Polar Express".
One foggy winter night in Chuggington, Thomas hears a noisy whistle. However, Koko, Wilson, Brewster, Hodge, Zephie, RJ and Fixer don't seem to notice it. When Thomas opens up his shed door, on the track near the repair shed, a fantasy magic train called The Polar Express pulls up in front of the repair shed. He is invited aboard by the train's mysterious conductor to journey to the North Pole. Though he initially hesitates, he joins the train after it starts to move.
He meets the train behind him, who is secretly named "Phantom". They must all overcome a variety of obstacles; at one point, a herd of caribou block the tracks. Later, the cotter pin holding the throttle together breaks. The train, now out of control and Thomas, Phantom with the conductor standing on the front, then reach "Glacier Gulch," an area with steep downhill grades. The three must hold on tightly as Phantom speeds through Glacier Gulch and onto a frozen lake (During the Glacier Gulch scenes, Thomas screams out of control as the train speeds up). The train tracks are frozen under the ice, and as a result, the conductor must guide the engineer and the fireman towards the other side of the lake as the ice breaks up behind them.
They then reach the North Pole, but Thomas accidently backs up and couples his back buffers up to the observation car which speeds up. Thomas travels from section to section of the North Pole's industrial area, first visiting the Control Center, then the Wrapping Hall, and finally a warehouse before he's airlifted back to the center of the city via air ship. As he watches the final preparations, Thomas is handpicked by Santa Claus to receive "The First Gift Of Christmas". Realizing that he could choose anything in the world, Thomas asks for a "Wilhelm Whistle"-sounding golden whistle (that only believers can hear) which he always wanted. Thomas watches as Santa takes off for his yearly delivery.
Thomas returns to Phantom, and the conductor punches letters into the backplate of his new nameplate. These letters spell some form of advice ("Believe" for Thomas respectively). As Phantom leaves, Thomas wonders about no Rudolph. His friends suggest they go back outside to find him, but it is too late. He is saddened by the loss of not seeing Rudolph, but is happy when he sees that Santa had already visited Koko, Wilson, Brewster and the rest of the trainees; as he are still sleeping, with presents in their sheds. When Phantom arrives at Thomas' shed, he says his goodbye to Phantom, who, in return, gives him an oil painting of Phantom, and waves from the doorway of his home as Phantom pulls away and whistles goodbye. On Christmas morning, Vee finds a small present hidden behind the Chuggington Christmas tree after all the others have been unwrapped. Eddie opens the present for Thomas and discovers that it is the whistle he always wanted, which Santa had found in his bag on his sleigh. When Thomas rings the whistle, both he and his trainee friends marvel at the beautiful sound; but because Vee longer believes in Santa Claus or Christmas, she does hear it. The last line in the movie repeats the same last line from the book:
"At one time, most of my friends could hear the bell, but as years passed, it fell silent for all of them. Even Koko, Wilson, Brewster, Hodge, Zephie, RJ and Fixer found one Christmas that they could no longer hear its awesome blast. Though I'm still staying, the whistle still blows for me, as it does for all who truly believe."