"Them" is the name used to refer to the secret organization that apparently controls the protagonist's Panopticon or possibly the League of Panopticons itself.
There not much known about them outside of them being the responsibles of Beatrice's captivity, their control over the 'Con's government and a private army that protects their databases on the Cell Gardens.
During the story is discovered that they had been investigating the Casket, probably to control its power as is believed to be the responsible of the Great Loss when the Arcadia Panopticon was destroyed when they opened it. however, they may also known about the existence of the mysterious Simeon, a being of legend capable of granting wishes to anybody he deems worthy, as at the end of the story it is revealed that the Casket was in fact, a portal to Simeon's dimension.