As the Steam Team prepares for the holiday season, Sir Topham Hatt brings them to the sheds and tells them good night. (Thomas, Edward, Henry, Gordon, James, Percy and Emily to Tidmouth Sheds and Toby to Arlesdale End) Thomas then tells the story of the first Christmas, with Molly as Mary, Edward as Joseph, Bertie as the angel Gabriel, Spencer as King Herod, and Luke as Baby Jesus.

Mary tells Joseph that their child is arranged to be built, even though she is a virgin. The angel Gabriel appears to them and explains that Mary will have the Son of God built at the Bethlehem Steamworks. The three wise engines (Henry, Arthur, and Murdoch) tell King Herod that they are going to give gold, frankincense, and myrrh (which Murdoch is re-gifting) to the King of the Jews. When Herod thinks that the gifts are for him, the men explain to him that they are for the infant. Herod becomes angry and claims that he will scrap the baby.

At the Bethlehem Engine Sheds, the innkeeper (Gordon) tells Mary and Joseph that he has plenty of berths available with brand new windows. However, when Mary runs out of water, he forces them to stay in the Carriage Shed. When Jesus, the newly built engine comes out for testing, notices his parents, and the three wise engines, along with the two shepherd engines (Donald and Douglas) come to see him. Even two musical engines (Peter Sam and Duncan) arrive at the scene as well. Mary and Joseph receive the gifts from the three wise engines and even the trucks that the two shepherd engines pulled along to visit.

As the story ends, the engines whistle into the night.