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.
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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! :)
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.
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.
In Pokemon Emerald, both the Root and Claw fossils can be obtained. One may be selected at Mirage Tower and the other will be found at the end of the Desert Underpass.
Find a Sandshrew in the desert at Route 111, 113, or the Mirage Tower, and evolve it into a Sandslash at level 22.