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If a Mirage Pokémon suffers critical damage, it reverts into data represented by hexagons floating in the air that then return to the system through the hologram generators. If there is an overwhelming amount of data for the generators to absorb - seen when the Mirage Mewtwo with the entire database written into it is destroyed - the system overloads and explosively crashes.
The system is also seen to be capable of creating mirages of other things besides Pokémon, as Dr. Yung used it to create a mirage of his Mirage Master
persona in order to misdirect suspicion from him being the Master's true identity.