I don't own Pokemon. That is the copyright of Satoshi Tajiri, Nintendo, and 4Kids Entertainment (possibly, I'm not sure if it still belongs to the last one with the new voice actors and such).
A Father's Regrets
I know to you, I'm more of a monster than the Pokemon. After all, the only time we ever met face-to-face, I was determined to stop at nothing to recapture Mewtwo and use his abilities to help me conquer the world.
But that still doesn't change the fact that I'm your father, and as such, find it my duty to ensure your protection. To that end, I've sent those three idiots of mine to trail you ever since you began your journey. Yes, they think they're there to steal your Pikachu, and yes, they're actually the cause of most of the trouble you've encountered in your travels, but as long as you're relatively safe from harm, I won't be reprimanding them for their actions (incompetent boobs that they are).
Recently, however, they've given me disturbing information that you've picked up a new traveling companion during your Sinnoh adventures: a beginning blue-haired female trainer who wishes to become a great Pokemon Coordinator like her mother. I know you have feelings for her, though they aren't precisely the same ones that you've had for Misty or May, and I'm certain you're wondering why you and she are so much alike: never having met your fathers, starting off with a Pokemon who didn't like you. Why, from what I've heard, the two of you even witnessed Legendaries on your first days as trainers (I must make a mental note to find out what they were, so that The Organization can steal them for me later). Well, I suppose I owe you an explanation:
Some time ago, I was obsessed with finding an heir to take over The Organization for me when I'm dead and in the grave. To that end, I became something of a playboy, hoping to impregnate woman in order to eventually obtain a successor worthy of taking over the mantle of Team Rocket. I suppose, in a way, that does make me the monster you believe me to be.
I only succeeded in impregnating two women, one from Pallet Town, the other from Twinleaf Town. Over the years, I've come to realize that the children that resulted from those affairs mean so much to me, not just as the future heirs of Team Rocket, but also my legacy upon this world. I'll do anything in my vast power to protect them. Hence, while my buffoons keep a lookout on you for me, I need you to do the same for her.
Take care of your half-sister, Ash. Dawn needs her brother to protect her.