The Molecular Destabilizer is a weapon that was designed to destroy atoms.
Quarry was freed from prison by Breach on Van Kleiss' command to retrieve the Molecular Destabilizer. Since Quarry was not made of organic matter, he was the only one able to enter the field and retrieve it.
However, instead of handing it over to Van Kleiss, he took it for himself and used it against Rex, with the ultimate goal of selling it to the highest bidder. Instead of destroying Rex's atoms, the machine destroyed Rex's nanites. When Rex gained his Block Party, he was able to shield himself from the machine's lasers and deflect them back at Quarry, destroying the weapon in the process.