After Viridian City is destroyed during a war between teams Time and Space, the player decides he has to stop both teams before they cause any further damage. He/she teams up with a pokemon trainer named Jonathan to defeat both teams.
During the first section of the game, the main antagonist is Team Space. About half way through the first section, Jonathan is almost killed by a mysterious pokemon. The player attacks it, but is instantly defeated by it.
After recovering, the two trainers countinue their journey. Eventually, they find the team space headquarters, and take it over.
With the defeat of Space, Team Time begins to take over Kanto. In the process, however, they destroy several towns. So the player decides he has to defeat them too.
In Lavender town, the player encounters several Time grunts, attacking a group of Cubone. The player beats the grunts in a pokemon battle. As the last one is defeated, he says "No... We need our sacrifice...".
The plot will progress after the player has visited Saffron City. There is an old man, standing at the entrance. At first, he thinks you are a grunt, and won't let you in to Saffron. However, when he sees Jonathan he seems to recognize him, and lets you in. In the city, there is a small building that stands out from the others. A boy and his sister inside are playing with four baby Treecko. When you talk to the boy, he will give you a strong Grovyle that you can ride on. When you talk to the girl, she will give you a Diglett, and explain that he will dig for you when you go to your backpack section called "side pokemon" and click on Diglett. When you leave the house, you see that some Team Time grunts got in to the village. They are burning it with angry Magcargo. You fight them, and win.
The Saffron City citizens hold a meeting, after the grunts have been driven out. They decide that they must leave the town to find somewhere safe, and they want the player to lead them. You accept, and the citizens leave Saffron.
You spend a long time looking for a safe place, but eventually find a route that Team Time has not. Diglett digs an underground area for the villagers to take cover in. You can now found your own team, and name it. You create the team uniform, including seperate male and female uniforms.
You and other team members can go on missions to defeat some of Times bases. You can request that almost any of your team members assist you on a mission.
On your 38th mission, you will encounter the strange pokemon again, this time in Lavender Town. It is fighting a baby Cubone, which is nearly dead. You and Jonathan team up with the Cubone to fight the pokemon. The pokemon is startled, and lets the Cubone go.
If you lose against the pokemon, then you start over on the mission. If you win, the pokemon slowly fades away.