You find yourself in your room, when you go downstairs your mother tells you that Professor Elm has something to talk to you about. When you arrive he asks if you can pick up an item from Mr. Pokemon, after you agree he lets you pick from Chikorita, Totodile and Cyndaquil to help you on this errand. You find out it’s a Pokemon egg, on your way back you meet a red haired boy who challenges you to a battle, after you defeat him and return to the lab you learn that the boy had stolen a Pokemon from Elm. When the professor sees the egg he is astonished, he allows you to keep the Pokemon and encourages you to test your skills by challenging the Gyms across the region.
You first travel to Violet City where Falkner resides, but before you could fight him you had to climb Sprout Tower and defeat the Elder Li at its top. After you defeat Falkner you travel south to Union Cave, after you exit you find yourself in Azalea Town. You find out from Kurt the Poke Ball Master that Team Rocket has reformed and are in Slowpoke Well cutting off the tails of Slowpokes. After you defeat and chase away Team Rocket you defeat Bugsy the town's Gym Leader. Before you enter Ilex Forest the the red haired boy (Your rival) challenges you to another battle, after he loses you enter the forest. Inside you capture two Farfetch’d who’s master gives you the HM Cut which allows you to exit the forest which leads to Goldenrod City.
You then defeat the gym leader Whitney and head north to Ecruteak City where in the Burned Tower you will meet the three legendary dog Pokemon, Morty and Eusine. After that you defeat the town's gym leader Morty and head west towards Olivine City. You learn the leader Jasmine is in the Glitter Lighthouse, after battling your way up you find out that “Amphy” is sick and she can’t leave his side. You travel to Cianwood City to receive medicine for Amphy and you defeat the cities leader Chuck. After you give Amphy the medicine you go to the gym and defeat Jasmine the gym leader.
After Jasmine’s defeat you go north east through Mt. Mortar and end up in Mahogany Town. Both the path farther east is block and the gym is blocked you head north towards the Lake of Rage. Inside the lake you fight a Red Gyarados and meet the current Pokemon league champion Lance who helps you to defeat Team Rocket in their secret base under Mahogany Town. You then defeat Pryce the gym leader and receive a call from Professor Elm who says that something is going on in the Goldenrod Radio Tower. When you arrive you realize that the tower has been taken over by Team Rocket, after going through and defeating Team Rockets new leader he decides to disband the group forever.
You then head back to Mahogany Town and go farther east to head into the Ice Path which leads into the final gym of Blackthorn City. When you beat the gym leader Clair she tells you that you must go into the Dragon’s Den and prove their worthiness to the elder. When the elder approves of you Clair gives you the badge, you then visit Professor Elm who gives you a Master Ball. After getting the ball you are informed that the 5 Kimono want to battle you to see if you're worthy of facing either Lugia or Ho-Oh depending on your games version. When you beat the five you travel to either the Whirl Islands or the Burned Tower to face your legendary Pokemon.
When you are done battling your legendary you are able to travel into the Kanto Region to go through Victory Road the final barrier between you and the Elite Four. When you reach the exit you face your rival for one more time, after his defeat he begins to understand why you are strong and he is not. When you exit you are faced with the Indigo Plateau, the place where the Elite Four and Champion reside to take on challengers. When you enter you first defeat Will a psychic master, then Koga a poison master, next Bruno a fighting master and finally Karen a dark user. After defeating her you face Lance the dragon master who helped you beat Team Rocket, after his defeat he congratulates you on becoming the Pokemon Champion and enters you into the hall of fame.
