The Universal Brotherhood was shut down before Chicago became Bug City, Glor. About a year before, IIRC. Ares and the UCAS (among others) were trying to quietly deal with the hives without causing a panic, after they'd been given evidence of the UB being a front for the bugs. The excuse given depended on the jurisdiction, but tax evasion was the most common one. Yeah, that's right. They brought the UB down allegedly for tax evasion. Hey, it worked for Capone, right? Anyways, with the UB officially shut down, Ares and others began moving against the hives, eliminating them where they could. When Ares raided an old warehouse that had belonged to the UB, searching for bugs, they uncovered the Chicago hive, and all hell broke loose. Not long after, Ares forces trapped inside the CZ used Damocles (AKA a small tactical nuke) inside the building the bugs had relocated to, resulting in the Cermak blast.
Since Bug City, the Universal Brotherhood doesn't exist. Period. There are some old abandoned chapterhouses, of course. And in one of the Missions (Brothers United, IIRC) you have a few old bug shamans trying to bring over a new queen. Oh, and then there's some of the insect shamans and queens that Ares has been experimenting on. More on that in Conspiracy Theories, a short story in Street Legends, and the upcoming Sacrificial Limb adventure.