You use the red orb to get groudon after you do that you can go to the top of Mt. Pyre (If you want to of course because I just wanted it to get out of my keyitems section) and give it to the old lady and you will see the boss of team magma.
When you get the scanner you can give it to capt stern he is in slateport city and he is in the fairy entrence.
The root fossil you can give to the devon corp to make it into a pokemon just go to the 2 floor of the devon corp and the third row of computers theirs a guy sitting their talk to him and he will tell you to come back later for your pokemon.
And about the rain its just scenery I guess