To team elemental: Here is how Pokemon Shadowstone will start:
As [player] comes out of his house, he goes to lab, overhears conversation about [professor] doing field work and tries to leave the town. He hears a "HEY!!!" and runs to 1st route. He sees [professor] being attacked by team azure grunts. His Pokemon is defeated. Then [rival] comes and says: 'Hey [player]! Guess what? I was told by [professor] to take theses Pokemon and- (cut off by team azure grunt) GO AWAY!!! WE DON'T NEED ANY MEDDLING KIDS!!! [rival]: Hey!!! You're attacking the professor!!! [player], take a pokemon, we'll battle them!!! (Battle ensues) What? How dare you beat my precious Munchlax! [rival] "Ha!!! good job, [player]!!! Not as good as me, of course!!!" (you go back to lab, prof. says good job, keep the Pokemon, blablabla, end.)
Next thing is, if I read it well, is to check whether or not mewtwo broke free. That could look like this:
Prof congratulates you, but then becomes more serious. "You saved me, but we have a problem far more complicated than some grunts kidnapping me." Problem of getting to the cerulean cave; I thought it might be able to go by boat, but If you can script it, another idea could be a 'flying'script with you and the prof on the back of the same pokemon.
Well, anyway, when you get there, people are standing there, astonished.
And then, he walks by. It's the team Azure boss. Even he seems to be wondering, but he also has an evil grin.
He sees the two of you, wonders why the prof is still running around freely, then leaves the scene. Then suddenly, everything is black.
Now, you can see mewtwo, and yourself. He speaks:
'You look wondered? Ah, yes, you are amazed. Relax. This is a dream, you áre asleep. I'm in your mind. And I'm going to give you a message, one you will not forget soon, maybe not even as long as you live. I am powerfull. Maybe the most powerfull creature on this planet. Universe. You created me. And therefore I owe you a thanks. But you made me a slave. You locked me up, you tried to use me. You forgot. I ám still powerfull. More powerfull than you. So I broke free. Again. And now, I will make sure that this was the last time I had to break free. You can no longer force me to be your slave. I am now free. Mewtwo is free. Mew? Mew is doomed.'
Light comes again, and you are surrounded by a lot of people.
What happened, asks the prof?
He understands before you speak. A vision, a dream.
You return to the lab. He sends you on a mission. Finding out what Team Azure's plans are, and keep an eye on mewtwo all the same.
Your journey, it starts there.