When the game first starts out you are fast asleep, your mother comes up stairs and she tells you that she has two things to tell you, one is to set the brand new clock she gave you and the seconds is that they are to attend a ceremony at a temple for Ho-oh, when you arrive at the temple, your mom tells you to wait outside for a moment and you notice something above you, and it is the legendary whose temple you are at and then it disappears, you wonder why you of all people saw it. Shorty, Team Rocket appears and ransacks the temple, stealing everything, Oak rushes out and hands you a poke ball and tells you to chase after the two Rocket grunts that are carrying everything. You approach them but before you can challenge them to a battle your best friend shows up and he beats one of them with you defeating the other. The grunts run away saying that Giovanni will get his revenge.
You return to Oak and tell him about the legendary and he takes you back to his lab and tells you that you have a bond with it and that you should keep your Pokemon as a gift. Your mother freaks out and grounds you, saying that you are too young to wander around the world alone. Determined to start your adventure, you run away and go to the nearest city where your best friend is now your rival who is angry that you witnessed the legendary before him. After the battle, you receive a letter from Oak that tells you that in order to find the temple where the legendary is, you must collect all the badges and defeat the elite four to prove your worth, but Oak warns that Team Rocket has placed spies in the gyms and in the elite four.
After beating half of the gyms, you rival informs you that Oak and your Mother have been kidnapped by Team Rocket and you must get them back. You now have to find the spy who is hidden in your home town. When you defeat him, you go to Team Rocket's base and fight Giovanni, who defeats you and informs you that he will use you to lure the legendary out. You are captured and thrown in a cell.
You escape with the help of your rival who was the real spy all along and wants to help you. You go and fight all the other gym leaders and along the way help towns out by ridding their town of Team Rocket. Once you get to the elite four, you are infamous among Team Rocket and as you are exiting Victory Road, they blow up the exit. Stuck in victory road, you turn around only to find a Pikachu staring at you (You can fight it but it is Level 100 and almost impossible to beat) you follow it as it runs away and it leads you to a hidden section of the map.
Once there, you chase after it to the center where there is a stone column and perched on top is the Legendary. You battle it, finally capturing it, you can now return to the exit, once there, Pikachu will reveal a secret exit. You now enter indigo Plateau and before you enter you have a short battle with your rival, once down to his last Pokemon the legendary springs out and the battle ends prematurely with him surrendering, he reveals that he was sent by Giovanni to capture the Pokemon and get rid of you. He then walks into Victory Road.
You now fight the elite four and once you are up to the champion, they reveal themselves as the spy and now fight you, part of the battle the spy will try and capture the legendary, after defeating them, the authorities arrive and arrest him. Prof. Oak and your mom are revealed and you now exchange a few sentences with Oak and your mom apologizes for having ever doubted you. The spy is thrown in Jail and you are crowned the new champion, the game goes to a black screen and the next thing you see is a newspaper with the headline "Team Rocket disbanded, *Insert Player's name here* crowned new champion!" You place down the paper and the you are challenged by a new comer who says he's going to be the next pokemon master. The credits roll as you accept the challenge.
