How to Get a Master Ball in Pokémon Ruby

Go to Lilycove City.

You must have been to Mt. Pyre to see the Blue Orb taken and witnessed the submarine being stolen from Slateport to do this.

Go to the Team Aqua Hideout in the north-east of Lilycove (you will need to use Surf) and keep heading north.

Enter through the door and you will see two white circles. These are teleporters.

Take the one on the left.

As you are taken to the next screen, you will see a teleporter to the south. Walk to it and take it.

Now take the teleporters to the left, left and left again.

When you reach the final row of teleporters, take the one farthest to the left.

You should reach a room with four item balls. The two on the right are Electrodes, be careful.

Pick up the Nugget and then you will be able to reach the Master Ball!