Departure season 3 centers on the mystery of The Queen of the Narrows ferry, destined for St. John's Newfoundland, which sinks in record time with most of its passengers on board. This has the whiff of a conspiracy, but is that really the case, or is this just another incident? Dominic Hayes and Kendra Malley, two investigating officers, are tasked with uncovering the truth.

The season's mystery begins with the derailing of the automated high-speed train Apollo on its way from Toronto to Chicago. At 140 mph, the train loses control at a tough turn and hits a tanker truck at a crossing. Seventy-two passengers are dead in total, including the driver, Walter Mack. On Howard's recommendation, crash investigator Kendra Malley and her assistant Theo fly to the other side of the pond to assist the FTSA in the investigation. They work with FBI agent Ellen, fellow computer geek Charlotte, and local sheriff Parker to break the case. Scotland Yard detective Dom joins in later in the investigation. The derailing of the train leads us to many tracks of mystery, and the mystery leads to a shocking revelation.