-In Pokemon Red/Blue, you assume the task of taking down the criminal syndicate to save Kanto. This is a harmless task, right? WRONG.
Giovanni was a poor man, so he set up Team Rocket to try and conquer Kanto, Sevii Islands and Johto. He failed miserably. He has a son you see, a son who he can support by succeeding in said criminal syndicate, but he fails. Fair enough Kanto is saved, but what about his poor son? His 7 year old son who he can't support?
Because of this failure, Giovanni takes on the Sevii Islands, and the evil child Red stops them there too, despite their best efforts.
What happens next? He spends 3 years establishing Team Rocket in Johto to try his luck there. By this point, his son is 10, but they are still poor. He steals a Pokemon from Elm's lab because, living a poor life, has grown up robbing to become successful, so because of this professor Elm calls the police. Not knowing that this poor boy has rejected his father's offer and just become a rough rebel just to survive another day. He sets himself an ambition, to become the champion, and you stop him from doing so. The current champion Lance also knocks sense into this poor boy's head and causes him to doubt his father's logic and lifestyle, but you still put him down. You're about to exit Victory Road, and he battles you, but because you beat him, he has to go back to the nearest Pokemon Center and heal his sick Pokemon (thankfully none of them die). He has to trudge to that nasty cave again because of your own personal gain.
At this point, you've also beaten Team Rocket in Johto, and Giovanni is in a cave listening to his minions' progress, listening to them fail. He has nowhere to go, and has no choice but to listen to his 3 year plan go to waste. He disappears from said cave and is never heard from again...
Silver is alone, and remains in Johto. Now, you're all happy in the Kanto region, stopping the last member of Team Rocket. After all this, you earn 7 gym badges and trek to the desolate island of Cinnibar and talk to none other than the broken 13 year old. You battle him in Viridian City, and you defeat him.
In the space of three years, you break an orphan and force him to fail everything he tries... twice... and you also try your best to keep Giovanni and his red haired son Silver a poor father and son.