When you get here, Kraden will say that Menardi mentioned a ship being here. If you've played the original Golden Sun you might remember Issac and co. coming here briefly, and attempting to get the ship to move, to no avail. You won't be using the ship here either.
After looking around (remember, Kraden and Jenna don't have the remarkable bird's-eye-view of the world that you do), they'll find the ship. The "thingie" that makes it go is that black orb, but you don't have it. Jenna will get annoyed at Kraden, and eventually Alex will show up. The fact that he managed to deal with the entirety of Lalivero and Tolbi in such a short space of time is quite impressive, but sadly he'll never join your party.
The screen will move to the yellow glow of the Venus Lighthouse's beacon. It's been fired, but now there's a huge earthquake as the foundations of Venus Lighthouse begin to collapse. As a player you will probably realise (where Jenna and Kraden don't) that since Venus is Earth then obviously unsealing the brute force of it would cause a earthquake and tearing of mountain ranges. Anyway, Idejima's now no longer connected to Gondowan now, and it will begin to drift away. Alex will reappear from the other side of the peninsula, and tell Jenna and Kraden to follow him. By some miracle, Felix and Sheba have actually survived!
Alex is more than a little surprised when he learns off the recovering Sheba that Saturos and Menardi were defeated by Issac and company. Sheba explains what her and Felix are doing here, and Alex will remark on there acutally being another continent out here. There's a short panic whilst they realise Idejima will drift north of it, but that turns into terror when a big bad tidal wave appears, on a direct collision course with you. It hits...
...and everyone's still alive. Great, because you'll be needing everyone (except Kraden). You can inspect yourself if you want, but make sure to talk to everyone before you go running off to the new continent (the tidal wave carried you here). You'll get an amusing few lines if you decided to leave everyone behind.
Alex has disappeared. Don't worry, but you won't be getting a Mercury Adept for quite a while, so get used to it. Sheba will explain that she has her own reasons for taking part on this quest. You'll decide to leave Idejima to explore the new continent. On the world map, turn the corner around the mountain range and head down to Daila.