After you beat Saturos and Menardi, you'll find yourself in Lavilero. You endure some more talking, then you go outside the house. Iodem comes out and gives you the Black Orb that controls the ship. Once you are in control again (when you can walk around again), head to the northwest part of Lavilero to the building that a soldier from Tolbi is guarding. Talk to him, and he'll let you through. Once inside, go west along the ledge at the bottom and north along the dock.
Use the Black Orb at the northern part of the dock to raise up the ship. You endure some more talking (boring!), everyone (Isaac, Garet, Ivan, and Mia) gets on the ship, the ship sets sail, and credits start rolling. After the credits are (finally!) done, it will say 'To Be Continued'. It will show what happened to Felix, Jenna, Sheba, Kraden, and Alex. After all of that is over, I suggest you get Golden Sun: The Lost Age. But if you have never had an opportunity to play it, I suggest you get the guide, or get a lot of FAQs online because the puzzles are torture! Especially Air's Rock. But it gets easier after you beat it for the first three to five times. By then, you probably won't need a guide. I'm not saying you'll need a guide to beat it, I'm just saying it gets frustrating sometimes. If you do get it, have fun!