Cargo Ship - FF7 Walkthrough
When you regain control of Cloud grab the nearby chest which contains an Ether. You'll notice an All Materia behind some crates too but Yuffie is blocking it right now. In order to advance the story forward you need to speak with your party who is currently in disguise around the ship.
After you've spoken with all of them you'll need to return to Aeris who then instructs you to find Barret. You'll find Barret at the front of the ship and speaking to him advances the story forward. Below is each of the steps and the location of each party member.
1. Speak to Yuffie (Cargo hold where you first began)
2. Speak to Aeris (Cargo hold just north of Yuffie)
3. Speak to Tifa (Lookout Platform on the deck of the ship)
4. Speak to Red XIII (The Soldier 'dancing' on the deck)
5. Return to Aeris (Cargo hold; same spot)
6. Speak to Barret (at the front of the ship)
Return to the Cargo hold and collect the All Materia before going through the door that is no longer blocked off. In this room you'll want to go up the ladder to your left immediately and run around the cat walk to collect Wind Slash, a weapon for Yuffie.
Only when you're ready to face off against the boss do you want to get close to the Shinra soldier standing near the terminal looking thing. I would highly recommend you have at least All + Restore on two characters so that you can keep your entire party alive very easily during this boss fight.
After the boss fight pick up the Ifrit Materia before you leave - you'll never be able to get it again if you miss it here. Exiting this room will dock you Costa del Sol, you'll regain control of your team in town.