What must you do when you find the submarine?

Assuming you are refering to after You kick Team Aqua/Magma out of their Lilycove City base, resurface and head through the Seafloor Cavern untill you find Kyogre/Groudon and fight Archie/Maxie.

If you mean when you find it underwater inside the cave in route 128 dive to the surface and you will find your self inside a cave.

There will be some Team Magma or Aqua depends on the version. Inside you will need Rock Smash and Strengh.

When you reach the end there will be a giant Pokemon get near and the leader of the Team will appear then he will battle you beat him and something will start to shine the Pokemon will wakeup and start moving the Pokemon will desappear and the leader of the opposing team will appear then you will be out of the cave looking at a catastrophy the leaders will go and then Steven Stone will appear telling you to go to Sootopolis where he thinks the problem is coming or something like that go to Sootopolis and Surf left go up and as far as you can there you will find Steven and the city gym leader they will tell you go into the Cave of Origin.

Go in and bring your strongest Pokemon with you because the Pokemon in this cave may give you Problems if not with a fast Pokemon to start with and scape. Also buy a bunch of Ultra Balls so you don't have to use the Master Ball you get at the hideout before then go deep in the cave you need Flash and when you get to the final room you will see the giant Pokemon again save before you battle with it then go in fron of it and your orb should start shinig there you will fight the giant Pokemon Kyogre or Groundon depends of versions.

Quote you MOST catch the Pokemon to continue with your progress or you won't be able to keep the normal game so save the game and use ULTRA balls only there is more stronger Pokemon that you will need the MASTER ball in use.

You welcome from Ninja boy Lao the evolution master.

After you find the sub, you have to dive up, then beat Team Magma/Aqua that's in there. The rest you have to figure out on your own, because i'm not to big on giving tons of info away.