In Gen1, there is a rumor that there was a war.
That's why Red's dad died and doesn't exist in the game.
Also, Green/Blue's parents died also, and Professor Oak adopted him.
Lt.Surge says "My pokemon helped me in the war(or something like that), also
I'm sorry if your childhood is now ruined, but remember, it's just a rumor.
The other theory is that their dad left a journey, so the main characters wants to be like their father, also leaving for a journey