Nowhere they go away.
the sapphire is in the warehouse and to find the second code go to the dotted hole and use cut on the door, hope this helps
You need to find the two passwords...
Team Rocket's Warehouse
The sapphire is located inside the cave called Dotted hole on Six Island but once you obtain it you must defeat a scientist in the rocket warehouse on Five Island to get it again.
Team rocket was on five island not six island first of all second of all there gone forever after you beat them in the rocket warehouse.
You can find the Lift Key in the Team Rocket Hideout on Pokemon FireRed. It is dropped by a Grunt on basement floor 4 after defeating him.
In Pokémon FireRed, you can find Nest Balls in Team Rocket's Hideout in Silph Co. and in Team Rocket's Warehouse on Five Island and you will also be given a Nest Ball from the Lady in the Water Path in which measures the sizes of Heracross trainers have captured and if the Heracross breaks a record then she will give you a Nest Ball.
give a porygon an up-grade to hold (found in team rocket warehouse) and trade it with a game that is leafgreen or firered but it has 2 have the national pokedex, or u can trade it 2 a more recent game
go to the team rocket warehouse swim in the right then go down until you find a boy standing near a high rock put a lemonade in the high rock then the boy will give you the metal coat..........
The rocket warehouse is in five isle meadow guarded by three rockets. If your Pokemon are level 58 or above you should be able to defeat them.
to get the second password for the warehouse, you need to go in to the dotted cave in island 5. and the pattern of the holles are forward,left,right. to amazement you find the sapphire, then some random guy takes it and says that he is gong to sell it to team rocket then tells you the second password
in the cave where the team rocket grunts are you need to beat the elite four first. good luck$$$$