He began working as a correctional officer (possibly Oz's first African American CO) in Oz in the early 1980s and is a very old-fashioned, conservative official. As described in the Journal of Augustus Hill, Glynn's philosophy of running a prison is based more on retribution than redemption and rehabilitation. As stated in the journal, the reasoning behind this is so that Glynn can one day be promoted to the position of Commissioner of Prisons. The journal also states that Glynn wishes to do this in order to one day become the states' first African American Governor. He runs the entire prison answering mainly to Governor James Devlin, a right-wing politician whom even Glynn has policy disagreements with at times. Throughout the series, we view his relationship with several staff members and prisoners as he is doing his best to maintain order within the prison. Throughout it all, Glynn is well respected by the staff and for the most part treats the prisoners as justly as need be.
When acts of violence occur in Oz, Glynn has a tendency to lead a harsh interrogation of the suspected inmates but is quick to file a crime as "unsolved" when there is not adequate enough evidence to convict someone. Glynn also tries to only make convictions on inmates that result in a major change of Oz's power structure. On violence between the inmates, Glynn is preventative when lives are at risk and quick to lock down and isolate specific inmates as a means of stopping a war. He never seems to favor one side of inmates in any war and is quick to inflict penalties upon the gang's leaders. When inmates misbehave in general, Glynn immediately orders the staff to place them in solitary as Glynn wants the inmates who cause the most trouble out of the general population for as long as he can keep them out. Solitary seems to be the most preferable punishment to Glynn as he is quick to send an inmate to Ad Seg when the prison rules have been somewhat violated. When obtaining inside information about acts of violence to occur in Oz, Glynn often cares less about the informants' motives in reporting it and uses the information to cause a lock down of the prison.
On the issue of prison rape, Glynn is not quick to investigate acts of sexual abuse and violence for two main reasons. First Glynn realizes rape will occur in prison, and secondly, Glynn sees the positive administrative standpoint of rape inside prison in the "leveling effect" it has upon the rape victims. Glynn feels that inmates who are victims of it less likely to be a discipline problem as presented when inmate Peter Schibetta, whom Glynn has a personal vendetta against, is raped on two different occasions. This attitude shocks Oz staff members such as Sister Peter Marie who remind Leo that he should take a more compassionate view about rape following the rape of his daughter.
Amongst the inmates, Glynn is feared due to his toughened law and order based attitude. Glynn's preference for the isolation ward, week-long lock downs, and harsh interrogation style helps him empower this fear. Unlike Tim McManus, he does not try to build a working relationship with the inmates to help them better themselves, rather he just cares that they are obedient of his command of the prison. Glynn seems to get along with the inmates who run the cafeteria as long as it is run in an efficient and respectable manner. In general though, Glynn treats the inmates as fairly as need be assuming they have not done anything to cross his path.
Amongst his staff, Glynn is well respected even by COs who have shown a dislike for Oz's minority inmates. When problems pertaining to COs and inmates arise, Glynn is quick to help his officers out whether it be keeping inmates who attack them in Solitary Confinement or preventing an investigation that could lead to the firing of one of his officers. This is mainly because Glynn feels that he and his staff must remain unified and see eye to eye as much as possible. Throughout the series, Glynn has disagreements with some of the higher ranking liberal staff members such as Tim McManus, Sister Pete, and Dr. Nathan but respects their vision and does what he can to meet them halfway on most issues. Overall, Glynn is focused on maintaining order amongst the inmates, stopping the drug trade, and convicting the inmates he can for crimes that they commit when sufficient evidence is present.
In season 1, Glynn initially attempts to get African American inmate Kareem Said to cool his rhetoric about the prison system by telling him "Don't fuck with me, my brother" as a means of telling him as one Black man to another not to cause any racial uprisings within Oz. In season 4, Glynn is asked to run as Devlin's Lieutenant Governor mainly because Alvah Case, a well respected African American law school dean is the Democratic candidate for Governor. Glynn agrees because he is as Conservative as Devlin on most every issue. At this point Glynn is also pressured to fire Tim McManus but does not do so until McManus commits a series of self-destructive and idiotic acts closed out by the singing of De Camptown Races, a blackface minstrel song at the funeral of a Black CO. During the campaign, Glynn also is pressured by fellow African American community activists to replace McManus with an African American Unit Manager. He does, but eventually McManus and inmate Kareem Said show evidence of corruption in Emerald City, which ends up getting McManus his job back.
Glynn's ethnicity is brought up once again in Season 6 when an associate of Governor Devlin, City Mayor Wilson Loewen is found guilty of aiding and abetting members of the White Supremacist organization the Ku Klux Klan in a 1963 murder of two young African American girls. A race riot breaks out in the city's African American neighborhoods and Glynn prevents one from breaking out in Oz immediately locking down the prison upon the news airing of the trial. When Loewen is sent to Oz, Glynn is forced by Devlin to place him in a safe housing unit with no African American inmates as a means of keeping Loewen alive until Devlin can eventually pardon him. Loewen arrives in Oz attempting to bring up good memories between he and Leo during the Governor campaign but Glynn disgusted by his crime states that their past relationship is now over as the courts have found him guilty. As Loewen pleads innocence, Glynn turns a deaf ear to his pleas causing Loewen to tell Glynn that as an African American male, he should realize the courts' decisions have not always been correct. While Glynn remains sensitive to racial statements throughout the series, he does not do anything that suggests he is favoring to any particular group in Oz, especially the African American prisoners.
As warden of Oz, Glynn carries out Devlin's orders and does what he can to manage the state's largest correctional facility. A new cell block, Emerald City, is opened up and run by a unit manager named Tim McManus. McManus is unlike the rest of the higher ranking staff at Oz in that he came in with a college education and never started off as a correctional officer. He is a liberal idealist with whom Glynn often disagrees. McManus has complete control of Em City from the commissioner but Glynn overrides some of his decisions at times. One decision in particular that is overruled is the addition of inmate Paul Markstrom to the population of Em City. Markstrom, according to the file, is a petty African American drug dealer that is supposedly related to Glynn, but in actuality he is an undercover narcotics detective looking to put a plug in the drug trade. Glynn is the only staff member who knows his true identity and this becomes a problem when the Italian inmates, led by Nino Schibetta, kill Markstrom. Throughout the season, McManus and Glynn both argue frequently over the methods of controlling the drug distribution amongst the inmates. Glynn believes in more lockdowns and shakedowns to stop the traffic while McManus believes more in addiction treatment. Glynn announces several new policies over the season that anger the majority of the prison population. The board of corrections has decided to ban smoking and conjugal visit privileges from the prisoners and Glynn while having some disagreements over the policies states that enforcement of these policies is more important than the agreement of these policies. Tim McManus is most vocal against Devlin's administration and states that a riot may very well occur in Oz. Adding to this tension is the arrival of inmate Kareem Saïd, a black Muslim who is incarcerated for arson. Saïd is a well known militant who poses a major threat to the staff, Homeboys, and the Aryan Brotherhood inmates.
Throughout the season several inmates die in Em City, mainly caught in the drug war between the Italian and Black inmates. This angers Governor Devlin who is already in the process of reinstating the death penalty. The death penalty is reinstated and as a result Homeboy leader Jefferson Keane is executed by the state for murdering some other inmates. Another inmate Donald Groves attempts to murder Glynn as he is trying to help the cause of Kareem Saïd. Groves instead kills African American CO Lawrence Smith and as a result he is sentenced to death. Groves' attempt on Glynn and murdering of a CO causes the other guards to begin randomly assaulting prisoners throughout Oz which is something that appalls Tim McManus. Glynn is urged by Dr. Nathan, the prison doctor and McManus to fire the guards for this, but Glynn instead just temporarily suspends various COs without pay as punishment. This decision angers staff investigator Lenny Burrano who explains to Leo that it is something they should not do as they both came up through the ranks as guards and realize the hardness and attitude that develop with the job. Glynn also is trying to put a plug in the drug trade and urges McManus to shut down the Italian inmates who control it the most. McManus does his best to do this by transferring all of the Italians with the exception of Schibetta out of Emerald City.
In the meantime, Kareem Saïd is organizing the Muslims and other inmates secretly and this gets Tim McManus to be greatly concerned about a riot. When disgraced Muslim Huseni Mershah claims that Saïd wants to start a riot, Glynn orders a shakedown of Emerald City that results in a weapons seizure from every inmate but Saïd. McManus' suspicions become true and the prisoners take over Em City taking the Guards hostage. Saïd has a gun (which an unknown Black CO gave to him) during the riot and uses it to cause the inmates inside to organize. With the help of Scott Ross, Ryan O'Reily, Simon Adebisi, and Miguel Alvarez, Saïd and the inmates make a list of demands to occur in order to release the guards who they have taken hostage. Glynn reads the demands and thinks that most of them are actually reasonable but Governor Devlin ardently opposes them and urges Leo to have the S.O.R.T. team use force to take back the prison. Tim McManus opposes this and goes into Em City with food for the prisoners in order to see how the hostages are doing. After McManus does not come back, Devlin has the S.O.R.T. team go in with machine guns and take back the cell block. As a result, 6 inmates and 2 correctional officers die and the rest of the prisoners are sent back to Gen Pop (With the exception of the riot leaders who were taken to Solitary). Tim McManus and several other staff members are greatly injured but live as they were accidentally shot during the take over.
The aftermath of the riot is investigated by Alvah Case, a law school dean whom Devlin has appointed to lead the investigation for purposes of clearing Devlin's hands. Throughout the investigation, Glynn and the staff are in the process of covering up the murder of inmate Scott Ross from Case. Ross was shot in the head, heart, and genitals and after interrogating several staff members, Case is convinced that CO Diane Wittlesey killed Ross. Glynn urges Case to leave it alone as Wittlesey is one of his best guards and Ross was one of the most dis likable prisoners in Em City to both the staff and inmates around him. Case concludes that the only way to get Devlin free from guilt in using force is to file no charges against any of the prisoners. Case states that the riot was caused directly by anti-prisoner acts passed through the Governor's office and that if the prisoners are guilty, Devlin is too. Devlin warns Case that he will not become the state's attorney general as a result but Case no longer wants the position as after investigating the prison conditions, he wants to run against Devlin for governor in the next election instead. Devlin is not supportive of this but goes through with it as Case announces to the press that no one in particular is at fault for the riot but improvements will be made to prevent another riot. This saves the job of Glynn and everyone else on the staff and also guarantees the reopening of Em City.
Emerald City is reopened 10 months after the riot under a new deal approved by Glynn and McManus. Ten inmate groups- The Muslims, Aryans, Homeboys, Latinos, Italians, Irish, Bikers, Gays, Christians, and Others will have four inmates from each group living in Em City and one representative from each group will be present on a Seg Council as a means of figuring out how to make life better for themselves and the staff inside of Oz. McManus starts a GED program which Glynn supports until Governor Devlin cuts it from the state budget. The program has positive results however particularly with inmate Arnold "Poet" Jackson whose talent for poetry brings a good name to Oz, a published book, and an early parole. This is short lived however as Poet violates parole and comes back to Oz for murdering a drug dealer whom he owed money.
In the meantime, Glynn has several issues. First, his daughter is raped at school by a gang of Latinos and this puts Glynn in complete disarray. A snide remark by inmate Miguel Alvarez during a speech that Glynn gives the inmates infuriates him and causes him to lash out on Alvarez sending him to solitary confinement. Sister Pete urges Glynn that he is a better man than that and that Miguel Alvarez was incarcerated at the time of the rape and not involved with the rape. Glynn lets Alvarez out of solitary then. Alvarez however knows the men responsible for the rape and tortures Glynn with this knowledge as revenge. In an interrogation Miguel won't tell Glynn the names of the men involved but does make comments pertaining to his daughter's rape. Glynn nearly assaults Alvarez but is stopped by Father Ray Mukada. This incident causes there to be bad blood between Glynn and Alvarez who later in the season blinds a Latino CO named Eugene Rivera. As a result Alvarez is sent to solitary by Glynn gladly.
The second major issue for Glynn this season is Italian inmate Peter Schibetta. Peter is the son of deceased leader Nino Schibetta and now runs the Italians with the help of Chucky Pancamo. Leo's brother Mark committed a murder for the mafia, and as a result Peter uses it as leverage to get what he wants from Glynn inside of Oz. Peter gets the kitchen from Leo and then tells Leo that he will pay the price if Mark does not turn himself in for the murder. Mark turns himself in after a talk with Leo who then furiously transfers the Italian inmates out of the kitchen and into the dress factory. Peter is later raped by Black inmate Simon Adebisi and Glynn is not unhappy about it as he wants Schibetta to suffer. Antonio Nappa comes to Oz to run the Italians, and with the help of the Italian staff members gets Glynn to take Adebisi off of heroin as a result.
Other issues that preside for Glynn in this season of Oz come in the form of Vernon Schillinger and Kareem Saïd. An inmate Alexander Vogel is murdered with the word "JEW" carved into his chest. Glynn quickly interrogates Schillinger, the leader of the Aryan Brotherhood. The interrogation does not yield any proof however giving Glynn a headache through Schillinger's obstinent and racist behavior (Schillinger tells Glynn that his "people", i.e. African Americans are as anti-semitic as the Brotherhood in addition to humming a blackface ministrel song praising slavery). Glynn finds proof however from gay inmate Richie Hanlon who is then forced to cop to Vogel's murder by Aryan Guard Karl Metzger. Schillinger thereby goes free which angers Glynn. During the Islamic month of Ramadan, Glynn announces that Governor Devlin is pardoning a Muslim inmate from Oz. Kareem Saïd is chosen but refuses at the press conference as he believes it is a cheap way of gaining Islamic voters throughout the state. Saïd stays in Oz, a move that shocks Glynn and Tim McManus.
This season starts out with issues pertaining to CO Karl Metzger. A number of incidents involving the Aryan Brotherhood have occurred and Tim McManus thinks Metzger is responsible. McManus' suspicions are true when it is discovered that Metzger used to belong to a White Supremacist organization and Glynn is urged to take action. Glynn refuses to take action until there is hard evidence that Metzger is working with Vernon Schillinger and the Aryans. This move surprises McManus who points out to Glynn that Metzger only thinks of Glynn as a Nigger. Chris Keller then comes forward and Vernon Schillinger is placed in solitary and Metzger is found murdered. Glynn later approves the hiring of Sean Murphy as the head CO of Emerald City who is a life long friend of Tim McManus. Murphy starts a boxing program in Oz where one inmate from each group will be represented in the boxing tournament. Meanwhile, Augustus Hill with the help of Kareem Saïd testifies against inmate Malcolm Coyle for murdering an Italian American family without getting caught. Glynn informs the DA but is too late as the Italians led by Antonio Nappa protect Hill through murdering Coyle. Glynn also must deal with letting Miguel Alvarez redeem himself for blinding Rivera by interactions with Sister Pete. In the midst of this, the Latinos are caught dealing drugs and after being unsuccessfully interrogated by Glynn, they make an attempt on the life of Miguel.
Glynn has a major issue when Clayton Hughes applies for a job at Oz. Hughes' father Samuel was an African American CO and Glynn's best friend who died working in Oz in 1982. As a result, Leo is the closest thing Clayton has to a father since Sam's death and he ardently refuses to hire Clayton as he fears for his safety. Leo hires Clayton however to the objections of his mother, Lenore as Clayton did well enough in CO training to be hired immediately in another State Prison. Glynn keeps a close eye on Clayton who ends up working in Em City. In Em City, Hughes messes up on more than one occasion and he is transferred to the library as a result. Glynn must also tell Hughes about the details pertaining to the death of Samuel and this puts Clayton in a very disturbed state. Things are made worse for Clayton when inmate Simon Adebisi tells him that it was a racially motivated killing of Samuel.
Throughout the season, Glynn must deal with Tim McManus and a rising racial tension inside of Oz. McManus is accused of sexually harassing CO Claire Howell and inmate Kenny Wangler. Because of McManus' sexual habits of bed hopping and womanizing, Glynn does not know what to believe and warns McManus that if any of this is true, he will be fired. Later, as Glynn confronts McManus for the "shit storms" he has created, McManus rebuts that Glynn's judgment is clouded for racial reasons. McManus points out to Leo that he has automatically taken the side of any Black inmate or staff member when issues pertaining to him arise and Glynn is extremely angered by this. At the same time the racial tension is on the rise in Oz due to the boxing tournament and a manipulative secret plan of black inmate Simon Adebisi. The boxing tournament is put on hold when the Aryan and Muslim inmates fight but Ryan O'Reily and Hamid Khan convince Glynn to let the finals happen. The finals end in tragedy fueling to the emotional fire between the inmates and Glynn is forced to lock down the prison. As Glynn puts the prison in lock down, Hughes comes to him stating that they should be helping the black inmates out instead of punishing them. Glynn then states he feels no sense of brotherhood towards any of the black inmates in Oz and then fires Hughes. As Hughes is fired and the prison is in lock down, Clayton gives Adebisi a gun as a going away gift.
Glynn ends the lock down telling the Black and White inmates separately that if one more racially motivated incident occurs, Oz will be permanently locked down. The Latinos in the mean time are not warned as they are somewhat neutral throughout the racial tension. Governor James Devlin's campaign manager then talks with Glynn telling Leo that he has been chosen as a candidate for Lieutenant Governor as their current Lieutenant Frank Feeley has throat cancer and will not be running for re-election. Glynn immediately asks if this is due to the fact that Alvah Case, a fellow African American has announced that he is running against Devlin. Devlin's campaign manager Wendy Schultz says it is a strong reason why Glynn has been chosen as there is a bad history between Devlin and the State's African American community. Racial issues aside, Schultz states that their office figures that someone as conservative and publicly known as Glynn would be a great candidate for Lieutenant Governor and Glynn then says yes suspiciously. In Oz, Glynn wants to stop the drug traffic as the Homeboys, Latinos, and Italians for the time being are allied so he gets a narcotics detective Johnny Basil to pose as a Jamaican drug dealer named Desmond Mobay. Glynn is the only one who knows Basil's true identity and informs him of the dangers associated with Oz as another undercover detective Paul Markstrom died many years earlier in Oz. Throughout the season Basil is somewhat convincing as Mobay to the point where he ends up snorting a lot of heroin and murdering an inmate to get in the good graces of all three gangster groups.
Adebisi then asks Glynn to move Black inmates Arnold "Poet" Jackson, Kenny Wangler, and Junior Pierce out of Unit B and into Em City as a means of ending some of the racial tension within Oz's walls. Tim McManus opposes this mainly because he hates Wangler for lying about a sexual harassment charge. Glynn is interested in eliminating racial issues within Oz and overrides McManus' objection. More racial issues arise however as those three inmates harass a new White inmate unfit for prison. Adebisi wanting revenge on Wangler gives a gun to this inmate Guillaume Tarrant who then shoots Wangler, Pierce and a Black CO Joseph Howard amongst others. Glynn is now under intense pressure to fire Tim McManus and solve the gun smuggling quickly as a means of making the prison look well managed during the election campaign. Adebisi and Muslim inmate Zahir Arif point out that McManus must go and a Black unit manager must be hired. Glynn does not yet give in as he still thinks McManus is competent and mentally sound enough to run Emerald City. McManus however is on a self-destructive path following recent relationship problems and sings De Camptown Races, a blackface minstrel song at the funeral of Joseph Howard, the Black CO who died in the shooting. As seen through earlier issues regarding race between McManus and Glynn, Leo draws the line with McManus here and immediately fires him as Unit Manager of Emerald City.
A problem arises when inmates Agamemnon Busmalis and Miguel Alvarez escape Oz through a tunnel and Glynn asks Raoul "El Cid" Hernandez, the Latinos leader who despises Alvarez to help find him. El Cid orders a hit on Alvarez who is now on the run. Meanwhile, when investigating the gun smuggling, Glynn is told by El Cid that Adebisi got the gun from Clayton Hughes on Hughes' last day of work. Glynn furiously calls in Clayton who admits to smuggling the gun and he has Hughes arrested as a result told to shut up in the meantime. Since being fired, Hughes has become a Black Militant and is giving speeches that condemn Governor Devlin on a routine basis. Busmalis is then captured and the Republican party then is looking better in the preliminary polls. The Muslim inmates then convince African American community leaders to pressure Glynn into hiring a Black unit manager for Em City, and he begins to listen more and more as a means of becoming Lieutenant Governor with the Black vote. Glynn then hires Martin Querns a Black man to run Em City appeasing the general public.
Martin Querns has experience working in several state detention centers and federal penitentiaries and is also from the ghetto like several of Oz's African American inmates. Querns is told he may run Em City any way he wishes as long as racial tension and violence are eliminated. Querns immediately reduces the violence by more than 92% and eliminates the racial tension element altogether. Although he has done this by empowering Simon Adebisi and his followers and sending most of the White inmates out of Em City, Glynn does not care as for the time being the Unit looks better managed. In the meantime Tim McManus undergoes psychiatric therapy and wants to run Em City again but the only available job in the Unit Manager position is Unit B which he reluctantly takes. During the campaign as order is maintained in Oz, Glynn stops paying attention to what changes are being made in Em City and is more focused on becoming the Lieutenant Governor. At a staff meeting, Tim McManus points out what has happened in Em City and Glynn turns a deaf ear as the violence has been almost eliminated from Em City. At a press conference shortly afterwards, Clayton Hughes goes psycho and tries to kill Governor Devlin. Devlin nearly dies, Hughes is charged with attempted murder, and Glynn drops out of the election race to stand by Clayton as he goes to trial.
Out of the election campaign, Glynn is brought more up to what has happened inside of Oz. Detective Johnny Basil turns himself in for the murder of Bruno Goergen as his conscience kicks in and tell him to stop doing what he is to prove that he is not undercover. Two inmates then die, both residents of Em City and Glynn begins to get angered with Querns. McManus points out that Querns has empowered Adebisi and the Homeboys in Em City turning a blind eye to their behavior as long as order is maintained. He points out the lack of diversity as all the COs are now Black and White inmates are also scarce. Finally he points out drugs are out of control as stopping the drug traffic is not a priority of Querns. Glynn isn't convinced of this until McManus with the help of Kareem Saïd brings him a videotape of a party inside of Adebisi's pod. Glynn is disgusted by the acts involving drugs, alcohol, and sex that the Black inmates are committing unpunished. As a result, Querns is immediately fired and Leo realizes he hasn't paid enough attention to what has happened in Oz. He gives McManus control of Em City once again and Adebisi then dies making a murder attempt on Kareem Saïd.
This half of the season starts out with the investigation of a news crew coming into Oz. Glynn is afraid that several dead issues will be resurrected through the media and is fearful that Oz may be shut down altogether. To make matters worse several inmates suggest what has happened during Adebisi's reign of power in Em City. Martin Querns then comes to Glynn asking him to destroy any evidence relating to the rampant drug use that occurred in Em City as a means of saving both of them from facing criminal charges. This news crew led by Jack Eldridge eventually agrees with Glynn that the story should not be aired and this is completed by a beating at the hands of inmate Cyril O'Reily. Even though the staff is glad that O'Reily scarred off the news crew, Cyril's behavior grows worse over the season and Glynn is urged by McManus to send him to a mental institute. Amongst the O'Reily's, Cyril's brother Ryan is accused by Muslim inmate Zahir Arif of murdering Patrick Keenan, an investigation that angers Glynn and frustrates Ryan. There is not enough evidence at the time however and Glynn must let O'Reily go free.
A number of new developments occur throughout this season however for Glynn. Oz is temporarily asked to house some illegal refugees from China who get caught up in a war between the Homeboys, Italians, and Latinos. This war escalates throughout the season to the point that inmates Supreme Allah and Enrique Morales are targeted to die by the Homeboy's new leader Burr Redding. Supreme is attacked in the visiting room at one point and later dies in the cafeteria all on acts devised by the Homeboys. Morales lives though and with the help of Chucky Pancamo the Italian's leader, makes numerous attempts on Redding throughout the season. Miguel Alvarez is recaptured near the Mexican border and comes back to Oz. Alvarez then makes a deal with Glynn to remain out of solitary. He agrees to be Glynn's informant in Em City if allowed to stay there. This is short lived however as Alvarez cannot get back into El Norte and find any useful information. Amongst the Black inmates, the Muslims now have a war with the Aryans and Bikers that gets ugly throughout the season. Brotherhood initiate Carl Jenkins makes an attempt on the life of Kareem Saïd but instead kills the newly converted Leroy Tidd. This murder angers Saïd who wants Aryan inmate James Robson to suffer for setting up the murder. When Glynn tells Saïd there is not enough evidence to convict Robson of killing Tidd, Saïd violently attacks Robson and Schillinger to the point where the entire prison is threatened with a lock down until a truce is called. The truce is short lived however when the Aryans threaten the parole of white inmate Tobias Beecher. Saïd stabs Schillinger and Robson and Glynn has the DA charge him with attempted murder.
During the season, Glynn hires a new secretary and hosts the regional Warden's conference. At home, his wife requests a divorce which puts Leo into disarray. It can be assumed that his wife is divorcing him because he exploited several details of their family issues while running for Lieutenant Governor. Martin Querns has been hired by the commissioner to be Warden at Lardner, the other main prison in the state and shows up at the conference. At the conference, Querns tells Glynn that Clayton Hughes who is serving his sentence at Lardner is doing horribly and will most likely die within the year. Glynn wants Hughes to serve his sentence protected and begs for him to be transferred to Oz. In Oz, Hughes serves time in Unit J, one of the safest units in the prison as it is the Unit for bad police officers. In that unit, Hughes serves time with Alvin Yood a small town sheriff imprisoned for assault and Detective Johnny Basil who is no longer under the alias of Desmond Mobay. Hughes is problem for both of them and kills Basil. This forces Glynn to transfer him to solitary which he manages to take over. In solitary Hughes goes psycho capturing and threatening to rape CO Travis Smith. As the SORT team attempts to recapture Hughes, Glynn goes in first to try and reason with him as a means of preventing Hughes from doing anything crazy. Clayton then tries to kill Glynn who is saved by inmate Greg Penders. The death of both Hughes and Basil, two of the only two inmates whom he had any considerable care for the well being of and the divorce from his wife puts Glynn into a bad state. Glynn is then seen drunk in his office distraught over the bad things that have happened and then considers resigning as Warden of Oz.
In this half of the season a baptist reverend named Jeremiah Cloutier comes to Oz for embezzlement. Cloutier is really a good person who is in Oz for stealing money, so Glynn privileges him more than the other prisoners. As a result Cloutier has a positive impact on several of Oz's inmates but is threatened by Catholic convert Timmy Kirk who is out to cause trouble. Kirk uses his conversion as an excuse to bully several Catholic inmates and then with the help of the Bikers gets Reverend Cloutier trapped into a wall that is being constructed. This gets worse when a gas explosion set up by Ryan O'Reily and IRA member Padraig Connolly destroys the cafeteria leaving Cloutier in third degree burns across his body. The kitchen and Em City are both destroyed and Glynn must send all the inmates to Gen Pop.
The kitchen and Emerald City are both rebuilt and in the rebuilding it is discovered that Reverend Cloutier has been engulfed in the explosion and is barely alive covered in third degree burns over the majority of his body. Also, the death of Patrick Keenan gets complicated as Ryan O'Reily pays and plays off two inmates against each other to state different stories. In reopening Emerald City, the prisoners in solitary are transferred in as repairs to the air ducts must be made. Glynn states to these prisoners that if they behave they do not have to return to solitary. A new liaison to the governor's office Eleanor O'Connor is hired to work at Oz. O'Connor coincidently is the ex-wife of Tim McManus. Upon the reopening of Em City, visits are allowed for the first time in months but this ends in tragedy as the bus transporting the visitors crashes near the entry gate. As Em City is reopened, the staff warns the Muslim and Aryan inmates to temporarily call a truce so that no blood is shed. Issues develop though when James Robson kills a young Muslim inmate Ahmad Lalar undetected. This war is stopped for the most part as Sister Pete has Kareem Saïd, Tobias Beecher, and Vernon Schillinger involved in various interaction sessions.
Glynn also sees that Peter Schibetta has finally been released from the psychiatric unit recovering from the raping received three years earlier by Simon Adebisi. Schibetta is not out for long though as he is raped for a second time as the Italians and Aryan Brotherhood go to war over the death of Hank Schillinger, Vern's son. When Sister Pete wants to help bring Schibetta's rapists to justice, she discovers how much Glynn really hates Schibetta as he states that "Here in Oz, rape has a leveling effect." This war causes a crippling blow to all of the Italians' current leaders causing a request to Glynn from Burr Redding to control the cafeteria. Glynn does not want the Homeboys to manage the cafeteria mainly because of the disastrous way it was ran under the management of Simon Adebisi. Redding convinces Glynn though that the Italians are currently unfit to manage the place and the Black inmates who are the majority of the staff are more likely to do a good job under his leadership so he is given control.
Glynn also deals with the issues pertaining to Reverend Cloutier this season. As he was badly burned in the gas explosion, the only inmate they can for the time being implicate is Jaz Hoyt as he was the head of the repair crew that trapped Cloutier. Things get complicated between Cloutier's flock, The Bikers, and inmate Timmy Kirk and Hoyt then after seeing a supposed vision confesses to a series of murders inside of Oz and ends up on death row. Kirk in the mean time is trying to cause trouble for Father Ray Mukada and hires inmate Clarence Seroy to set up a burning of the rectory in which Mukada resides. Glynn is angered by this and with help from the Bikers, gets Kirk moved to death row. Reverend Cloutier's body ends up missing though and leaves the staff baffled.
Glynn later sees that McManus is engaging two new programs for the inmates to help rehabilitate themselves. He is starting a singing program with the help of Ryan O'Reily's mother and a guide dog program from a woman named Alicia Hinden. Both programs have positive results especially for inmates Omar White and Miguel Alvarez, two inmates the staff have almost no hope or belief in. Alvarez is on an upward trend coming into his parole hearing which Tim McManus supports. Glynn ardently refuses to acknowledge Alvarez's attempts at rehabilitation and tells the parole board to do everything in their power not to let him go. The board is successful as Alvarez gets agitated and strikes Luis Ruiz, the only Latino on the board during the hearing. Glynn shortly afterwards gets evidence from Tobias Beecher implicating Vernon Schillinger in the raping of inmates Franklin Winthrop and Adam Guenzel. As a result, Glynn sentences Vern to solitary for an undecided length of time.
The final season of Oz begins for Glynn with the bi-annual solitary review. In this review, it is decided whether or not to release the solitary inmates back into the general population. Miguel Alvarez, Greg Penders, Vern Schillinger, Omar White, Carlos Martinez, and Henry Stanton are up for review and voted on by Glynn and the staff. Being that Glynn cares about his officers, he refuses to let Martinez and Penders out of solitary as the two of them are in for attacking COs. Omar White then remains in solitary as well. Stanton and Schillinger are released as with Miguel Alvarez whom Tim McManus insisted upon releasing into Emerald City. Glynn then sees that an associate of his, Mayor Wilson Loewen is on trial for assisting the Ku Klux Klan in a racially motivated killing of two African American girls in 1963. This trial causes a race riot in the city's African American neighborhoods and a lockdown of Oz whose Black inmates are angered at the mere presence of the trial. As the SORT team locks the prison down, they discover the dead body of Tobias Beecher's father who died at the hands of Franklin Winthrop.
The trial of Wilson Loewen ends with him being found guilty of murder in the second degree. Loewen is a key politician that helped Governor Devlin get elected so Devlin is very insistent on how Loewen will be carefully handled when he gets sent to prison. Devlin has Loewen sent to Oz to placate and appease the African American mob that has formed. Devlin has an unannounced intention of pardoning him as the racial tension outside of Oz cools down. In Oz, Devlin insists that he be placed in the safest unit which happens to be Unit J, the bad police unit which currently has no African American inmates. As Glynn sees Loewen arriving to prison, Loewen tells him that he is innocent but Glynn does not care as the courts have found him guilty. Loewen then pleas that as a Black man, Glynn should realize that the court's decisions aren't always correct. Loewen is in Oz safely until he blackmails Governor Devlin for a pardon. Devlin then uses his African American assistant Perry Loftus to secretly cause the death of Loewen and then handpicks police detectives to help keep their hands clean from the murder. However, Glynn, Tim McManus, Eleanor O'Connor and Detective McGorry figure out that it is Loftus and CO Adrian Johnson who are responsible for the deaths of Loewen and other inmates who know about the murder. Shortly after wards, O'Connor and Glynn have an affair which shocks McManus. As suspicions grow, Johnson has inmate Lionel Kelsch murder Glynn the night before the lifetime achievement award ceremony. Glynn's murder causes Tim McManus to put together every possible piece of evidence to convict Devlin of the whole conspiracy that took place. In the meantime, Martin Querns is named as his replacement at Warden.