Batman must board the Gotham Rail Train with Ra's Al Ghul to slow it down while Jim Gordon destroys the railroad tracks to ensure the train never meets its destination. He was using Jonathan Crane AKA The Scarecrow as a puppet as part of his big plan to purge Gotham into a city of fear until it rips itself apart. In the final act of Batman Begins, Bruce's trainer and mentor Henri Ducard is revealed to be the true Ra's Al Ghul, the twisted leader of the League Of Shadows.