In Pokémon Emerald, Mirage Tower will appear in the Desert that is to the North of Mauville City however it will only appear once you have spoken to the Ruin Maniac in Fallarbor Town. Once you head into the Mirage Tower, you will need to use the Bike that is the Mach Spike because of the various sensitive cracks in the floors. However once you have picked 1 of the Fossils then it (the Mirage Tower) will disappear and it will not return at all.
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In Pokemon Emerald, The Mirage Tower appears randomly. All you have to do to make it appear is keep going back-and-forth from Fiery Path to the Desert and it should appear. Just make sure you have the Mach Bike, You'll need it inside the tower to get past the fragile sand floors. And at the end of the Mirage Tower, you'll get a nice suprise! :)
It will disappear and reappear in the desert on Route 111 as the player visits and leaves the Route.Do not confuse it with Mirage Island.
In mirage tower ( at desert near route 111)
Mirage Tower is in the desert around the enterance near Mauville. It only appears every once in awhile. I'm not sure how often though.
Well when you acquire one of the fossils in the desert the other fossil you didn't choose will appear in mirage tower so it can be either the root fossil or claw fossil.