There are a few plans that Team Aqua is working on.
First plan is the building of a submarine. To this end they will try and corner a prominent engineer at the Slateport Oceanic Museum to capture this Engineer and have him build them a submarine. If the abduction is successful they will have him create the submarine back in their secret cave headquarters near Lilycove City. If the abduction is unsuccessful, Team Aqua will commandeer the Scientist's own submarine.
The second plan is to find pokemon that are strong in rain. To this end they will send Admin Shelly to launch an attack on the Weather Institute on Route 119. They will do so with the purpose of taking the Institute's supply of Castform, a pokemon that can predict and affect the weather in small ways, and to take control of the Institute's weather control project.
The third part happens after the first and second plans are attempted (no matter if Team Aqua was successful or not). They will attempt to kidnap a meteor scientist and have him unearth a powerful meteor with which they will use to make dormant the nearby volcano, allowing rain to fill the volcano. Coincidentally this is done at the same time Team Magma try and kidnap the same meteor scientist so they can get the meteorite but to use its power to enhance the volcano instead of making it dormant. Team Aqua will send Admin Matt to kidnap the scientist.
The fourth plan is after the third plan. They steal the Blue Orb from Mt. Pyre. They use the submarine, (the one they build or the one they commandeer depending on how events play out during the campaign.) to dive down into the ocean and find Kyogre's hidden chambers using the Orb (the orb glows brighter the closer you get to Kyogre). They will try to unleash Kyogre and it's ability to make endless rain onto the world. They will learn the error of their ways when Kyogre proves to be too strong and is making things worse with its endless rain.