Summary:

In the year 2008, the Federal Transit Authority of the United States was called on by the Boston Subway to investigate the abnormal situation of Boston Subway Blue Line Train 784, which had been reported running on almost every line in the rapid transit network. Shortly after, reports rush in of the same train appearing on various other subway and rapid transit systems in the U.S. 

No one knows how this train can switch from one subway system to another, let alone pilot itself [as there was no previously specified autopilot mode attached to the train]. Therefore, the FTA sends in investigator Nicholas Arnelli to board Train 784 and get to the end of the line with this abnormal situation.