Father Mukada's season began with him accompanying inmate family members to Oz for a visit. While on the bus he meets Morales' sister's who's provocative demeanor makes Father Mukada a little uncomfortable. He also chats with Carrie Schillinger who asks him to bless baby Jewel in an attempt to remove the family "curse" that tormented Jewel's father (Schillinger's son). As the bus proceeds, it swerves to miss an on-coming truck and the bus overturns. Father Mukada emerges from the bus, bloodied and scarred but it turns out, that he's possibly the only survivor. Once he's recovered, he returns to Oz and tries to get to the bottom of Jim Burns' murder and Cloutier's imprisonment in the wall. He discovers that Timmy Kirk is more than likely responsible. When Mukada confronts Kirk, Kirk of course denies all of it. The tables turn when Timmy Kirk's attacked by Hoyt and while he's recuperating, Kirk asks to return to Mukada's flock. Mukada flatly refuses. Kirk, now bent on revenge, gets an inmate to arrange for Father Mukada's parish house to burn in a fire. This results in Mukada getting hospitalized with serious injuries.
Season 4 Part 2
Upon returning from a retreat, Father Ray hears about new inmate Rev. Cloutier converting inmates. Father Mukada learns Timmy Kirk--one of his altar boys-- has joined Rev. Cloutier's flock. Mukada meets with Cloutier to discuss this matter. After a quietly confrontational discussion with Cloutier, Father Mukada finally decides to plan an ecumenical service that will include inmates of all faiths, even Rev. Cloutier's, whom he's still skeptical about.
Season 4 Part 1
Still reeling from Alvarez's escape, he turns his attentions to Sister Pete, who has now confessed that she wants out of the nunnery. Stunned Father Ray keeps surpresses his feelings but eventually tells her to do what's best. He soon hears a confessional from Keller, who is seeking complete absolution for past crimes. When asked for this absolution, Father Ray refuses because he doesn't believe that Keller is sincere in his desire to truly earn absolution and commit to the catholic faith. Keller curses Father Ray and leaves.
While delivering the Communion to Miguel, Father Ray discovers that Miguel hasn't eaten in days because the hacks aren't feeding him. Father Ray attempts to sneak food to Miguel, only to have it backfire on him as Miguel refuses to eat. Father Ray expresses to Sister Pete his feelings of being shut out when she initiated her victim offender program without including him. He also intervenes on Clayton Hughes' behalf to find out who killed Clayton's dad. Finally, he hears Sister Pete's confession that ends with her deciding to leave the nunnery.
Although somewhat frayed from the riot, Mukada returns to OZ. After unsuccessful attempts to find soon-to be-freed child molester Sipple help on the outside, he agrees to let him remain working and living in OZ, with horrific results. An encounter with inmate Shirley Bellinger makes Father Ray even more anxious, and to top it all off, he's taken hostage by Miguel after a viscious attack.
Father Mukada's a fair man who tries to keep his flock in Oz as spiritually sound as possible. He tries to keep an open mind but sometimes his personal feelings can get in the way. New inmate Alvarez provides one of many challenges to this but Father Ray does what he can to help guide Alvarez. Mukada arranges for Miguel to meet his father and grandfather both of whom are Oz lifers. The bond between he and Miguel gets tested when the riot breaks out and Miguel is put in charge of the hostages, one of whom is Father Ray.