Lise's adventure begins with her showing her students how to defeat a pink bird. Press to attack and to use a special attack when the bar at the bottom fills up and turns green. The bird has a lot of HP, but don't worry about dying; if the bird does manage to kill you, your students will cheer you on and bring you back to life.
After killing the bird, you will see a cutscene and regain control of Lise in the castle. Go directly north into the throne room and talk to the king. Then go through the door in the northeast corner of the room. Now go down the stairs in the southeast corner of this room. Now you will be in a long room. Go to the far east side of this room and then go north and talk to the guard blocking the door there. Now go back up the staircase that led you into this room (it's on the far west side of the room and goes north-south, not east-west). Now you should be in a room that has two doors leading north, go in the door on the right and talk to the old woman there. Now you will see a cutscene that reveals some of Lise's past and then reveals Elliot's current location.
When you regain control of Lise, go north back into the king's room. There are staircases going down to the southeast and southwest of the king; go down one of them (they lead to the same room) and then continue south to go outside the castle. Now head east and you should recognize the area where you just saw Elliot. Go south and go through the doorway to your west. Use the goddess statue to heal and save and then go down the stairs and through the door at the bottom to get to Elliot. You're too late to stop the ninjas' evil plan, and Lise is in such a rush to get to the king that she leaves Elliot behind...
When you regain control of Lise, head back to the king's room while killing all the ninjas along the way (if you don't remember how to get there, go out the door to the south, then go west until you see a big doorway, then go in it and keep going north). If you try going back to get Elliot, you will find that he and the ninjas are already gone.
After you get to the throne room, you will see a few cutscenes and then the credits will roll.