The stolen submarine at Slateport and Team Aqua's Hideout

From the Pokemon Center in Slateport, head north to the end of town and then right to Slateport Harbor.

Talk to Captain Stern, then Archie will announce he is stealing the submarine.

Enter the harbor, talk to Archie, and he will escape in the submarine.

Head to Lilycove City, then travel east to the water.

Surf on the water and head north into the cave entrance to find Aqua's hideout.

Inside the hideout, defeat the trainer: Team Aqua Grunt (Poochyena, Level 32, $640).

Use the warp panel on the right in the next room to find a Max Elixir.

Return and use the other warp panel. In the room with three Team Aqua grunts, you can battle them individually or as a double battle: Team Aqua Grunt (Carvanha, Level 32, $640), Team Aqua Grunt (Zubat, Level 31, Carvanha, Level 31, $620), Team Aqua Grunt (Poochyena, Level 31, Zubat, Level 31, $620). A double battle yields $1240.

Find the warp panel near the double battle grunts, but instead, go to the bottom left corner of the room to find another warp panel.

Take the warp panel on the right in the next room, then the middle panel in the following room, then the left panel in the next room.

In the room with four item balls, the two on the right are fake Electrodes (Level 30). The two on the left contain a Nugget and the Master Ball.

Backtrack: take the right warp panel, then the middle one, then the left panel to return to the first three-warp-panel room (you are on the right one).

Take the top warp panel. Head right to where the two Team Aqua grunts were and use the warp panel there.

In the next room, battle the Team Aqua Grunt (Carvanha, Level 32, $640).

Take the warp panel next to the grunt to find a Nest Ball. Return.

Take the other warp panel in the room. Go through the opening and battle the Aqua grunt (Zubat, Level 32, $640).

Go through the opening to the right and battle the two Aqua grunts: Team Aqua Grunt (Zubat, Level 32, $640) and Team Aqua Grunt (Carvanha, Level 32, $640). A double battle yields $1280.

Step through the warp panel in front of them to battle Aqua Admin Matt (Golbat, Level 34, Mightyena, Level 34, $1360).

After the battle, head right and step through the lower warp panel to return to the first warp panel room.

Go through the opening in front of you to return to the main room. Surf across the water to exit the hideout.

You can now head to Mossdeep City via Route 124.