Well, here's what I really think:
Around ten years after what happened in the 4th movie, Samuel Oak became a great Pok?mon researcher. Mrs. Boss, leader of Team Rocket, had this information, and made Samuel think she were a good woman. Samuel was in love with her and went to Viridian with her. Samuel was helping her with the Team Rocket technology but don't knew that he was doing evil things. They had a son, called Giovanni. After Giovanni's birth, Mrs. Boss wanted to give him to an orphanate, but Samuel got the child and runned off. He finally found a place called Pallet Town and lived there all his life. When Giovanni just grew, he met Delia and the two had a relationship, where Ash born. But after that, Mrs. Boss was too sick and almost dying (sp?), so, she said that if Giovanni didn't come to control the Team Rocket, she would kill his son. Giovanni had to go to Viridian and Delia had to tell Ash that his father was just a trainer trying to became the best Pok?mon trainer, what made Ash try to be the best too, since he was a baby. Meanwhile, in Viridian City, Team Rocket caught a Ho-oH. Giovanni asked for the god of the skyes to protect his son, for all his life. After some time, Giovanni was becoming evil, he met a Rocket, had a daughter called Daisy and a son called Gary. Giovanni wanted to leave his sons somewhere, and let them in Pallet, to live with his father. After around twelve years, he called for Gary to leader the Viridian City Gym, because he went to some kind of training somewhere.