Attack of the Fanboy

Pokemon Omega Ruby And Alpha Sapphire Guide – Team Aqua/Magma Secret Base

by Dean James


Throughout Pokemon Omega Ruby and Alpha Sapphire, the player will come into contact with Team Aqua and Team Magma on numerous occasions, though one of the largest involves taking down their secret hideout prior to the seventh gym battle. With a little bit confusing hideout and plenty of battles to come across, it seemed like a good idea to bring you a guide on how to conquer them. Playing Alpha Sapphire only, this guide is based on fighting against Team Aqua, but the two are pretty comparable, with the base basically being a reflection of the other.

Team Aqua Grunt

-Mightyena – Level 36 (Dark)

Team Aqua Grunt

-Carvanha – Level 34 (Water/Dark)

-Golbat – Level 34 (Poison/Flying)

Prior to the battles, a submarine will have been stolen and will be modded by the opposing team. That means you must not travel back to Lilycove City to take down Team Aqua or Magma’s hideout. To make it easy, you will ride back in a sub with Stern automatically.

Once in Lilycove, head to the right side of town and surf into the cave to the northeast, which will take you to the actual secret hideout for Team Aqua/Team Magma.

As said above, for the purposes of this guide, all information will be based on Alpha Sapphire and Team Aqua. The layout may be a little different, but is still relatively similar here with almost a reverse layout of the other. The Pokemon used are pretty comparative between the two, except for Carvanha, Grimer, and Sharpedo being used by Team Aqua instead of Koffing, Numel, and Camerupt that are used by Team Magma.

After entering the base, use the first teleporter you see to find a Nugget and then go back to the original area. Now go to the only other teleporter on the floor, where you will find a Grunt to fight.

Team Aqua Grunt

-Grimer – Level 35 (Poison)

-Carvanha – Level 35 (Water/Dark)

After that fight, there is one more Grunt battle on this floor.

Team Aqua Grunt

-Golbat – Level 37 (Poison/Flying)

The one other teleporter in this room will take you to a room full of beds, as well as a few Grunts. However, these will not challenge you to battle, though there is a Poke Ball with a Full Restore in it on the left side of the room. Return back to the previous room and go down the stairs in the northwest.

To the south is another Poke Ball, this time with an Escape Rope, along with a trainer who you cannot battle. Continue to the west and battle the Grunt you see.

Team Aqua Grunt

-Mightyena – Level 34 (Dark)

-Golbat – Level 36 (Poison/Flying)

Go north where you will see a scientist that you cannot battle. Head to the transporter on the right in this room, which will lead you to a Max Elixir in a Poke Ball. Return to the previous room and ignore the transporter on the upper left, as it leads to nothing. Instead, go to the one on the bottom left.

When in the next room, go north to find a Nest Ball. Then enter the left transporter in this upper area to find a PP Max. Walk directly right and into the transporter, which is followed by one other transporter. You will find TM97 Dark Pulse in this room and then return back two rooms prior. Walk to the bottom of the area and head east, where you will find a Grunt to battle.

Team Aqua Grunt

-Carvanha – Level 35 (Water/Dark)

-Grimer – Level 35 (Poison)

Head north and into the transporter, which will lead to a room with two more transporters and a Grunt. Challenge the Grunt first of all.

Team Aqua Grunt

-Mightyena – Level 27 (Dark)

Enter the transporter to the south for a very annoying puzzle. Use the following transporter sequence to get to the end: Right, Middle, Left, Left. After entering this room, head to the northeast part and you will find four Poke Balls. These consist of two Electrodes to battle, a Nugget, and most importantly a Master Ball.

Get back past the transporter puzzle and go into the right transporter past the Grunt you already faced. In this new room, you will see a Grunt right away who you should fight.

Team Aqua Grunt

-Carvanha – Level 37 (Water/Dark)

Keep going right and you will be forced into a battle with five Team Aqua Grunts at once, so it would be wise to have a Pokemon in the lead with an attack that can target all opponents at once.

Team Aqua Grunts

-Poochyena x5 – Level 18 (Dark)

After the battle, you will find a Max Revive in a Poke Ball on the bottom right. As soon as you move north, Team Aqua Admin Matt will challenge you to a battle, which is much easier than it should be for facing an Admin.

Aqua Admin Matt


-Sharpedo – Level 39 (Water/Dark)

After defeating Aqua Admin Matt, head to the north and west to follow the pathway to get out of the building and then you can head towards Mossdeep City for the next gym battle.

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