Walkthrough:The Legend of Zelda: Spirit Tracks/Black Dragon Laguz/Part 2

Now Alfonzo will ask if you're ready to leave. Tell him yes, and then your train will move out. Alfonzo will teach you how to control the train. What you have to do is get to Hyrule Castle before time runs out. Remember to watch out for other trains. You can see what direction they are heading, if you look at your map. Also, the other trains move a little slower than Link's train. Once you get close to Hyrule Castle, shift your train gearbox to the part that has two lines on it. Once you reach Hyrule Castle, you can shift the gearbox to reverse and this will stop the train. Once you do this, Alfonzo and Link will enter Hyrule Castle town.