One peaceful morning in starting town, the player wakes up and is told by his/her mother that Professor Tree is looking for him. The player goes to Prof. Tree's lab to find that Prof. Tree is not there, but Lauren/Vincent is. Lauren/Vincent gives you your starter Pokemon, and then the Prof. (who's not too nice) comes in and Lauren/Vincent gets in trouble (he yells at him/her). The Prof. apologizes about this to you. He gives you your Pokeballs and Pokedex and asks you to record data, etc. Then, in town 2, you meet your rival. He has a Pokemon from a different region, and somehow got to this region. Eventually, in town 5, you encounter Team Galactic for the first time. In the middle of the cave in the town, you find them using Cresselia's energy to try and create a new universe. You lose to Leader of Team (even if you win, he'll heal his Pokemon somehow and battle again until you lose or something) and then Lauren/Vincent comes to rescue you and turns out to be the player from D/P/Pt, and says upon appearing, "do these guys ever learn?"
Or something like that. That paragraph is simply a compilation of random thoughts :F