I was going to beat Flannery and I was at Meteor Falls where Team Aqua runs Team Magma out. After I talked to the scientist I left the mountain and went down a one way ledge all the way back to Rustboro city. However I don't think I can get back since Briney (the boat captain) is not at his cabin. Is there any way to get back without the boat?
I'm not quite sure I understand the scenario. But if you have rock smash you should be able to go through the cave where you first found Briney now.
Edit: I'm pretty sure you need to have rock smash in the first place to get to meteor falls and back to Rustboro city, so this should be the solution. If you need help finding the cave I'm talking about, let me know.
After jumping down the ledge south of Meteor Falls, you will end up in Rustboro. This means you will have to backtrack through Rusturf Tunnel and the Route 111 desert to return to Fallarbor. (Of course, this is obviously assuming you do not have HM2 Fly yet. And while I tested it on Emerald, it should also be true for Ruby and Sapphire.)