I would be more than delighted to help. Lets see..
It all depends where you are at. Here is the part I believe you are stuck at:
Go to the warehouse (mideast, right on the harbor) and go into it and talk to Dock. He'll tell you that the Doctor is missing. Then go to the Museum (there are rumors circulating that if you use a certain cheat at this time you can eat chicken in the museum which is totally false) and go talk to the scientists. Team Aqua will appear and when you fight them the doctor will return when they leave. Then you will be able to head to Mauville. Just to help you with Mauville, since I always get confused with this, New Mauville is just a short surf off the coast by the bike trail. I'll help you more with that later.