He is an African American prison guard who has a vast experience of handling various prison units. He is hired by Warden Leo Glynn after he is asked to find a competent black unit manager to replace Tim McManus. He is also a former drug dealer who would be in the same cells as several of the Homeboys had he been caught. In his experience controlling prisons, maintaining order is the top priority. He has also believed that drugged out prisoners were preferable as they became too weak to cause any discipline problems. As a result, he empowers the drug dealing heads of Em City, especially Simon Adebisi, to maintain order in exchange for doing and selling all the drugs they wish. Kareem Said, a militant Muslim inmate whom Querns despises and sees as a threat to prison officials, tells McManus what he's up to, and they collaborate to get videotapes of the drugs to get him fired. Querns is promoted to warden at the second main prison, which he manages until he gets rehired at Oz as the warden when Glynn dies.
Querns announces that there will be a system of three trustees who will maintain order within Em City among. He names Adebisi, Pancamo, and Morales as trustees, currying favor with inmates and drawing suspicion from head CO Sean Murphy. He then transfers out eight prisoners he thinks are potential discipline problems. The inmates are all either members of the Aryan Brotherhood or Bikers — white inmates who hate blacks — so the racial tension element is automatically reduced. Murphy calls Querns crazy for allowing the "three worst motherfuckers in this place" to be trustees and creating inequality by getting the most visible white inmates kicked out of Em City. Querns then transfers Murphy out as the head CO and replaces him with a black CO named Travis Smith. All the inmates who come into Em City are handpicked by Adebisi and Querns, who tells Warden Glynn that several COs are too supportive of Sean Murphy and McManus, and need to be exchanged as well. However, all of the new COs and inmates are Black and Glynn then assigns one white CO named Claire Howell, a sadist who hates Tim McManus, to work in Em City as well.
In the meantime, Querns is investigating some previous acts of violence to make sure it stops. He is caught up with Ryan O'Reily and Nikolai Stanislofsky, who are suspects in the murder of an inmate who had a smuggled cell phone. Stanislofsky opens up after Querns gets harsh in the investigation, and is granted a stay in protective custody. Querns ends up liking Stanislofsky enough to tell O'Reily that whatever happens to him will be his fault when he returns from Protective Custody. O'Reily then has Howell kill Stanislofsky in the hospital so that he can be free of any blame. Meanwhile, the Muslims are angered that Adebisi and his followers are allowed to use drugs and commit sodomy with no punishments. Em City has become overwhelmingly black, to the point that the Italian and Latino inmates are now a threat as Adebisi cheats them out of the drug business. They are transferred out and names Supreme Allah and Poet, two of Adebisi's key enforcers their replacements as trustees. Vern Schillinger, the head of the Aryans, tells McManus that Em City is out of control and could corrupt Unit B. McManus is sickened by Schillinger's suggestion to create an all-white unit but is even more sickened by the behavior in Em City. Querns is unmoved, however, as long as there is no violence in the prison. McManus almost quits before Kareem Said approaches him with a plan to stop Adebisi and Querns.
Glynn has been running for lieutenant governor, but stopped because after James Devlin is nearly assassinated by former CO Clayton Hughes. As a result, he has not been focused on Em City and has not seen what has happened. Things get complicated for Querns when O'Reily and his erstwhile partner-in-crime Chris Keller kill inmate Nate Shemin to get Querns fired and return the prison to "normal." They then kill Mondo Browne in the cafeteria, a move that angers Querns, as one of Adebisi's followers is now dead. Homeboy and trustee Supreme Allah is framed for the murders and Querns allows Adebisi and the black COs to beat him into submission before he goes to solitary. Querns' credibility is now at stake. Said then gets ahold of some video tapes showing Adebisi's behavior and delivers them to McManus, who shows Glynn. Querns is immediately fired. Angered, Adebisi tries to kill Said, but the plan backfires; Said kills Adebisi in self defense.
Querns later throws up as Cyril O'Reily is dying in the electric chair. Tobias Beecher then kills Vernon Schillinger in the prison production of Macbeth with a knife that was supposed to be a prop. Querns and prison psychiatrist Sister Peter Marie conclude it was an accidental death. The Aryan Brotherhood on staff in the mailroom opens a package with an unknown substance that kills everyone there. As a result, Warden Querns evacuates the entire prison.