Pick a Save Slot
To start the game, turn on Contact DS and press the F1 key on the touch screen to start a new game. Choose a game slot by tapping the corresponding key on the touch screen. If there is already a saved game in that slot, it will ask you a couple of times if you are sure that you really want to delete it.
Meet the Professor
When you start, you will see a mostly bald man typing at a computer screen. Tap on him with the stylus to get his attention. When he asks you to do it again, tap him again.
He'll ask if he has the right name for you (I'm pretty sure it's the name that you set in the DS settings.) If you want a different name, say no (tap the orange head or use the directional pad to select the orange head.)
Then he'll ask you for your home town. You can put whatever you want here. For example, you can put the name of the city or town you live in. You can select the 2 near the top of the screen to switch to the keyboard with accented characters.
Don't panic when it says INSUFFICIENT DATA. This is just a joke. Enter your hobby when he prompts you. He'll also ask you for your favorite food, your least favorite food, and a secret.
The guy says that he has been sending out a signal for many years, and sees that you are using a DS to contact him.
He needs your help, because some people are after him. He says that you can even pretend that it's just a game. An alarm sounds, and then you see a starry sky, where an orange light is chasing an green light.
The title of the game shows up. Then there is a somewhat surreal sequence with a boy chasing a girl.
The boy catches her, and she asks if the boy wants to hang out for a while. His default name is Terry. You can change it if you want. In this walkthrough I will call him Terry.
You'll see Terry sleeping on a bench. Apparently the weird sequence with the girl was just a dream. Terry looks up at the sky, where the orange light is attacking the professor's ship. A green crystal falls from the sky and lands near Terry. A pixellated ship lands, and the professor steps out, rushes over and takes the crystal. The orange light shoots past. The professor tells Terry to hurry and get into his ship. It takes off, and the orange light chases the professor's ship again, shooting it and eventually hitting it.
Meanwhile Terry's mom tries to call him, but the phone says "the number you have dialed is currently in space..."
The game automatically saves, and afterward, Terry is lying facedown on a beach. This is the Deserted Isle.