You start off in Niko's house in Aboda Village, where he is busy giving Link a history lesson of New Hyrule which serves as part of the introduction to the whole story. Of course, Link sleeps through the entire history lesson, much like an earlier version of Link slept through Niko's slideshow recap of events from The Wind Waker at the beginning of Phantom Hourglass. Soon Alfonzo appears, roughly shaking Link awake and reminding him he has an appointment in Hyrule Castle Town for his graduation ceremony. Leave the house and head for the lady's house on your right to clear all the rocks from the front of her house. She will reward you with some rupees.
Now head north to the train station. You'll now have to get the train to the Castle Town train station by yourself in 300 seconds. This part can be considered a tutorial on how to use the train controls. Use the train whistle to blow the Moink out of your way, then use the train tracks switch to switch directions as you watch how the other trains move along the routes. Continuing at top speed, you're going to switch to the right, then to the left, then to the right, then to the left. Use the brake when you reach Castle Town station.
At Castle Town, proceed north to the archway where you'll see a mailbox to your left. Tap on the mailbox, and you'll see a mailman come along and deliver a message to you. You can read the letter if you want, but it's not really necessary. Now proceed north and talk to the guards who will let you enter the castle. Continue north and you'll talk to another guard who will give Link some grief until the strangely double-hatted Chancellor Cole appears and tells the guard to step aside. Continue north and then you'll enter a cutscene in the throne room where Princess Zelda flirts a bit with Link before presenting him with the engineer's certificate. She will also slip him a letter that she wants him to read secretly. Chancellor Cole sneers at Link after the ceremony ends and he and Zelda depart, telling him he won't be using his train for very long.
After you get the letter, head south and read the letter, noting the location of Princess Zelda's bedroom and marking it on your map. Follow the directions toward her bedroom, and she will secretly ask for your help in getting to the Tower of Spirits. She will also give you a Recruit Uniform to make him look like one of the guards so he can move about the castle without being spotted.
Now comes the part of getting Zelda out of the castle. In the first room you enter with her, let her follow you around, keeping out of sight of the two guards as you watch them move back and forth, and then guide her to the door on the bottom right corner. Outside in the castle grounds, there are four guards that Link must distract. With the first two guards, go as Link alone and have them turn towards you away from where you want Zelda to go, then draw a path for Zelda to travel until she is safely out of sight. The third guard will require Link to distract by throwing a rock and having him move away toward you while quickly drawing a path for Zelda to scoot by unnoticed. The fourth guard can simply be distracted like the first two, giving you time to guide Zelda out through the archway before you depart.
With Zelda now out of the castle, head toward the station where you'll enter a lengthy cutscene period where she talks with Alfonzo, requiring his assistance to go to the Tower of Spirits. On their way there, however, the Spirit Tracks disappear, and Link brings the train to a screeching halt before he, Zelda, and Alfonzo see the tower break up into pieces floating in the air. Then a black demon train engine will roll over Link and Zelda's heads, and Chancellor Cole will appear with a masked man named Byrne to reveal his true self and his intentions with Zelda. Alfonzo bravely tries to defend Zelda, but is quickly overpowered by Byrne, who also easily slaps Link away. Chancellor Cole zaps Zelda, and her spirit departs from her body before Byrne carries it away, with Link helplessly watching before he faints.
Link will appear back at the castle in the infirmary to tell Teacher that Princess Zelda has been kidnapped. Alfonzo is now laid up from his injuries and tells Link he is now responsible for the care of the Princess. Now leave the infirmary and head south and toward the right, and Link will see Zelda's spirit taking form, trying to communicate with the guards and not being able to. Follow her through the throne room and into her bedroom, where she will ask Link to take her to the Tower of Spirits. She will also give him the Spirit Flute, a musical instrument that will come in handy throughout the game. To use the Spirit Flute, slide the pipes left and right with the touch screen and blow into the microphone to blow into the pipes.
Zelda will tell you there's a back way you can go to get to the tower. Leave the bedroom, go to the left side door in the throne room, and go through the upper door to get to the back exit of the castle. A guard will stop Link from leaving that way, saying it's too dangerous to go out without a sword. Talk to the guard and he will give you directions to the training room in the castle where you can get a sword. Mark the location on your map and follow the directions to the training room. Speak to the guard captain about getting a sword and he will give you one; however, you must go through a tutorial on how to use the sword before you leave with it. Pass the tutorial and then go back to the back exit where you talked with the guard, and he will let you pass through now.