The Seafloor Cavern is in route 128, south of Mossdeep City. You need to use dive to access it.
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It is in the cave where Archie of Team Aqua tries to capture Kyogre. Alas you need HM Dive to get there.
You find a Vulpix on the big tower west of Lilycove… You know, where Archie and T/A are.You can also catch Duskull, another good Pokemon. They are at about Level29-33.
bring it to the top of mt.pier and you will see archie. he is retrning the red orb. go up to the lady and retrn the blue orb now. and......thats it.
Archie will return the Red orb himself. As you are on the top of mt. Pyre, you should return the blue orb too.
To open the Cave of Origin in Pokémon Emerald, you must first go underwater to the Seafloor Cavern. There you must defeat Archie.