In Operation: Z.E.R.O., it was stolen from the museum by Father and used to restore the personality, memories, and powers of the Ultimate Evil, Grandfather. After the ensuing chaos at the Convention Center, the Recommissioning Module was given to Numbuh 1 by Numbuh 101, who used it (along with the KNDNA Tracker) to locate and recommission Numbuh 0, who turned out to be none other than his own father. Later, Nigel and his dad use it again to temporarily restore the personalities of Sector Z.
After Grandfather was defeated once and for all, Numbuh 1 tried to use the Recommissioning Module on his father once again. However, it burst into pieces, revealing a message left by Monty explaining that, knowing his son would try to bring back Numbuh 0 again, he had broken the Recommissioning Module himself, as he has responsibilities only an adult can properly do: namely, being a good father to his son. Numbuh 1 accepted this fate, but it is unknown if the Recommissioning Module was recovered and put on display once again.
It is never explained why the Recommissioning Module was able to resurrect Grandfather, since he obviously was not a KND Operative. It is possible that Numbuh 0 defeated his father with a Decommissioning device to erase his memories, or that Grandfather was a KND Operative in a previous era of the organization prior to becoming the global tyrant seen in the cartoon.
It is also unknown if this module is the only one in existence, as strongly implied in Operation: Z.E.R.O., or, as both Numbuh Zero and Numbuh 999 were decommissioned after the module's destruction, there are more.