The Team Aqua boss is in the Team Aqua's HQ. After attaining the Magma Emblem, and getting through the Team Magma's HQ off of Jagged Pass, go to Slateport City. There CPT. Stern will be in an interview, talking about his submarine. Then, Team Aqua will steal the submarine. After that, fly to Lilycove, and go on the beach. Instead of going to the right, (you can't anyways because of the Wailmer,) go straight. There you'll find a cave entrance. This is Team Aqua's HQ. After many trial and error attempts on the warp panels, you will eventually find the Team Aqua's Admin Matt. Battle him. Once your done, leave the hideout. Now you can go to Mossdeep city by Surfing. I'd suggest stocking up on repels if you want to get there in a hurry. Use the Pokemon Center to heal and save, before heading to a house that's north-west. In it, you'll find a fisherman who'll give you a Super rod. Now it's time to defeat the Gym LEADERS. They're twins who use Psychic-type pokemon. Level 41, Claydol. Level 41, Xatu. Level 42, Lunatone. Level 42, Solrock. Organize your team well, if you don't you'll get extremely frustrated when they're constantly 'confused' and/or 'asleep'. IMPORTANT: SAVE BEFORE YOU BATLLE THEM!!! Once your done, head to the Pokemon Center, heal, and save. Now head east ----> you'll notice Team Magma is there, surrounding their leader, and heading north to the Rocket Launching Facility. ALSO IMPORTANT: ONCE YOU GO IN, DON'T START BATTLING UNTIL YOU TALK TO THE SCIENTISTS. ONE WILL GIVE YOU A SUN STONE - VERY. VALUABLE!!! Battle through the grunts. Eventually you'll come across Team Magma's Leader Maxie..and STEVEN!?!?! Well...the rest is pretty straight forward. After your battle, you'll visit Steven's house which is on the island. There he'll give you the HM08, Dive. Now's a good time to start training, so use your Match Call to revisit trainers who'd like a rematch. TRAIN TRAIN TRAIN. Your next destination is Route 127, where you will dive unda da sea. It's a short distance south until you find Team Aqua's Hideout, which is also a cave. Battle the grunts blah blah blah. NOW. THE BOULDER PUZZLE. THIS INFORMATION WAS GOTTEN FROM http://www.supercheats.com/guides/pokemon-emerald/settling-things-with-team-aqua
SO IF YOU'D RATHER FOLLOW THE UNNOFICIAL GUIDE, GO AHEAD AND CLICK THAT LINK. OTHERWISE:
(1) Facing the first three boulders, move the left and right ones one space north.
(2) Now push the third boulder (what was the middle one) to the left one space, and step into the gap in the line of boulders you have created.
(3) Push the center boulder (the one you are faxing to the north) one space north and ONLY one space! Now carefully step into the space it was previously occupying.
(4) Push the boulders on your left and right to the left and right one space.
(5) Now step one space right and push the boulder to the north one space north; step two spaces left and push the boulder to the north one space north.
(6) Step one space north and push the boulder to your right one space east (to the right) thus clearing the path to the exit! Good on ya! You made that look dead simple mate!
Once you go back outside, someones there waiting for you. Guess who. Steven. And he's not happy. Here you have two choices. Fly to Lilycove and stock up things, or just follow him to Sootopolis.
FROM HERE YOUR JUST GOING TO HAVE TO FOLLOW THAT GUIDE BECAUSE I CAN'T TYPE ALL THAT OR COPY AND PASTE IT ALL WITHOUT GETTING IN TROUBLE. ONCE AGAIN, I DON'T OWN THE BOULDER PUZZLE, THAT BELONGS TO http://www.supercheats.com/guides/pokemon-emerald/settling-things-with-team-aqua
HOPE THIS HELPED!
The Team Aqua boss is in the Team Aqua Hideout northeast of Lilycove City. You will need the HM move Surf to reach the hideout.
You need to get past the Team Aqua grunts at Lilycove Town to advance on Pokemon Emerald. In order to do this, you first have to beat Team Aqua grunts at Lilycove Town.
after getting into team magmas hideout
at there hide out
In the Aqua headquarters there are grunts and the admin Shelly and Matt.Everyone else is at the Mt.Pyre.
he is at the top of team aqua HQ, after you beat him you get the master ball
team aqua boss is in underwater base near soatapolis city and pacidflog town
Just go to the hide out of team magma then fight the boss then go to lilicove city then go to the cave to the upper part where the 3 wailmer is there then surf and fight the boss of team aqua the the 3 wailmers disappeared after u fought the leader of team aqua.
there is no team aqua on ruby. Aqua is only on Sapphire and emerald. :) :) :) :) :) :) :) :)
I dont have the game but I think you have to battle the Boss pokemon.
The Team Aqua boss is in the Team Aqua Hideout northeast of Lilycove City. You will need the HM move Surf to reach the hideout.
You don't
In Lilycove city, travel east and surf a bit, you will get to Team Aqua's base. Defeat the boss and you will get a scene.
every where team aqua is or in snoop dogs house.
You need to get past the Team Aqua grunts at Lilycove Town to advance on Pokemon Emerald. In order to do this, you first have to beat Team Aqua grunts at Lilycove Town.
after getting into team magmas hideout
In team aqua's base