A thunderstorm causes damage on the Island of Sodor and results in a shipment to Mr. Jolly's Chocolate Factory going missing. Thomas is assigned with recovering the lost shipments, and to do so, he must help his friends along the way by completing fetch quests and minigames. He helps Harvey install a new hook so that he can rescue Edward, helps Percy find his mail cargo in a "haunted" mineshaft, and others. Upon finding the lost shipment, Thomas must rush to Brendam Docks to deliver the cargo before Bulstrode the boat leaves the dock.