Ok, there is alot you need to do before you can go to mosdeep city. Here is a list of steps that must be taken.
- Take the magma emblem to jagged path(by lavaridge town) and in the middle of the place a cave will appear when you go there. This is the team Magma hideout and you need to complete this area first. In there you will see maxie awakening groundon where it will flee. Then you have to defeat maxie and his Pokemon are tough(lvl. 37-39) so make sure you are prepared.
- After you defeat the magma hideout, you go to slateport city to the submarine port area where youll find a large croud surrounding the place. Gabby and Tye will be interviewing Captain Stern. During the interview you will see team aqua take the submarine.
- After this, you will go back to lilycove city and enter the team aqua hideout in the northeast corner of the city. You will have to defeat this place. You know you'll be done with this place once you defeat a fat aqua guy named matt. Once defeated, he will flee with the submarine. While you're in there make sure you find the master ball, which will be very helpful later on.
- After you defeat the team aqua hideout, the wailmers that are blocking your path will be gone.
- From there, surf through route 124 and you will eventually reach mosdeep city.
Source: experience (ive probably beaten emerald at least 15 times)
If you have any more questions, just comment and I will answer.