Across the Ocean Blue
You'll find everyone aboard the cargo ship, in disguise though. You'll find a guard guarding the door to the north as well as an All materia to the west near the crates (if you already have Yuffie, you won't be able to get it right now). Head upstairs and talk to everyone, save your game in the Save Point next to Red XIII, and buy a Super Drink for the merchant sailor. Head back downstairs and speak to Aeris, who'll ask you if you've seen Barret.
Head back upstairs and you'll find that the sailor to the west is no longer there, thus giving you passage to the western area. Go there and you'll find Barret snooping on Rufus and Heideggar. Talk to him from the west and an alarm will then sound.
Head downstairs and you'll find that all the sailors have been killed, including the one formerly guarding the door to the north. Assemble a party and go through that now accessible door. Upon entering, you'll be greeted by the maniacal Sephiroth, who'll soon dive skyward, leaving behind the JenovaBirth boss. Summon spells work best on it, but avoid Poison.
After the battle, seize the Ifrit materia that has just appeared, then head back to the deck. The ship then continues to sail west towards the West Continent.