I am stuck in Lilycove City

Go to slateport and find capt sturn above the pokemon center then talk to him and then go back to lilycove and go back in it and poof there gone

if u have a ghost cheat use it some how

You're most likely missing a key event in the story, reason why it won't let you progress. Just backtrack a bit, it'll come to you.

Go to lavaridge town with your magma emblem. Then go up to jagged pass. Your emblem should open up team magmas hideout and continue through till you beat The magma leader. Then go back to slateport and go to the crowded harbor. Hope it helped!

It happened the same to me because I used the "hall of fame" gameshark and the game thinks that I have already pass the game so I couldn't find the captain...
Waht I did is to use the "walk trough walls" GS code
It worked perfectly!

Talk to both of them. They would say something about their boss going off to hijack a submarine. Fly to Slateport City( if you have the HM) and go to the place where is the harbor and you will see captain stern being interviewed by two reporters. And then team aqua will talk through a microphone and then after you finish talking and all, go back to the team aqua hideout. You can now pass the place ( Remember there is also a Master Ball in one of the rooms so remember to check the rooms carefully!). Hope this helps!

The same thing happened to me over the past year. Stern won't show up, and the evil team base doesn't open up. Must be a game bug so you have to start a new save file...

You have to go and do the Pokemon battle tent and then go check, they will let you in. ;)

Bro when you are about to reach lilycove city there will be safari zone just front of it there will be water surf there little front of it you'll get a cave inside ther are two part go left one and go top ther will be team aqua solve it and the old lady ther will give you maa emblem and go that place where team magma took the meteorite go down stairs when you go little down the magma emblem will began shaking and a cave will appear go inside it fight team magma and team aquela in lilycove city inside that cave

First you need to go to mt.pyre which is at the entrance of lilycove(where there are so many trainers)then go find a dock,use your hm surf to explore that area and you will find a cave entrance,go inside it and you will find a exit in the left side,now go to the top of the mt. Pyre and defeat team aqua members,after that talk to the old woman and she will give you a magma emblem,now fly to where the team aqua and team magma fought,the lavaridge mountain,get to the bottom of it,and a cave entrance will open,defeat maxie at the end of that cave and get to the slateport you will find cap stern getting interviewed by reporter and after that his submarine get stolen by team aqua go back to lylicove and there(sorry if that wasn't very detailed)