A typical day at St. Thomas parish sees Ray being thrown out of a city council meeting for over-zealously arguing to save the church's soup kitchen from extinction. In the confessional, Ray ignores Church policy when counseling a distraught young woman who wonders whether she'll be damned to Hell if she has an abortion. As a result, Ray lands in an impossible, political, painfully public moral quagmire. When Ray is called to break up a fight at the parish school, he reaches out to a desperate teenage boy whose stepmother happens to be an old flame of Ray's and his one true love before he entered the priesthood. Her sudden reappearance further complicates Ray's life with all-too-human desires, and places him in the middle of a deeply emotional family crisis.
When Father Ray goes to battle for the church soup kitchen and invites a local politician to dine with the homeless on J.A.'s wedding day, his intentions for inclusion and human compassion are noble, but his timing couldn't be worse; and nuptial plans go horribly awry when J.A.'s check to the party hall bounces, forcing him to hold the reception at St. Thomas -- with a few more guests than expected.
Father Ray struggles to fulfill the last wishes of a deceased parishioner while her widowed husband, a lapsed Catholic who despises Ray, vehemently objects. Meanwhile, good fortune gives way to greed when a winning lottery ticket is anonymously left in the weekly collection plate.
Ray and Leo are painfully and angrily divided when Rachel (Tamara Mello) asks them for advice on whether or not to continue her pregnancy.
Even a priest needs a break from time to time, and when Father Ray takes a day off from his duties at St. Thomas he finds divine inspiration at a pick-up basketball game; while Leo deeply ponders his purpose in life.
Distracted by Father Leo's absence, Father Ray finds it mysteriously difficult to get in touch with God; while his old flame (Wendy Gazelle) returns to plan St. Thomas' Halloween bash.
Sibling rivalry is taken to extremes when Father Ray grudgingly opens his home to his estranged parolee brother. Meanwhile, Eric teaches an arrogant young seminarian a lesson in tolerance, and Mo gets her first opportunity to preach.
Father Ray attempts to save the life of a young man who has been hospitalized for speaking in foreign tongues and seeing spiritual visions. Meanwhile, Rachel is approached by a teenage girl (Kimberly McCullough) for advice about premarital sex and Eric develops feelings for a young musician with a checkered past.
Father Ray tries to end the violence between two warring gangs and is shocked to learn why a teenage girl is caught in the literal and figurative crossfire. Meanwhile, Mo helps Sidney reconsider his motivation for leaving his wife, and an unexpected and very welcome guest miraculously returns to St. Thomas.
Father Ray facilitates the inevitable dissolution of a broken marriage in a family besieged by alcoholism, violence and bitterness. Meanwhile, the staff at St. Thomas discovers that gifts sometimes do come in large packages when an elderly couple leaves their home to the Church.
Father Ray declares St. Thomas a sanctuary to a family of Salvadoran refugees on Christmas Eve and lands himself in the most unexpected of places to find a priest on a holy holiday. Meanwhile, the staff cannot agree on who will perform the Christmas homily.
The St. Thomas staff is taken to task when the Bishop sends Father Ray some very unwelcome assistance in the form of Father Martin. Meanwhile, a young black parishioner raises serious questions about whether he is welcome in the Catholic church.
When Mo is shaken by the sudden death of Sister Sebastian and confronted with Father Martin's plan to make staffing changes at St. Thomas, she strongly reconsiders her desire to remain a nun.
Father Ray's heroic instincts are aroused when Justine (Jennifer Beals) is accosted by a mentally disabled parishioner her first day on the job as St. Thomas' new Director of Education. Meanwhile, Justine gets involved in a power play between Martin and Ray over the fate of the soup kitchen.
Ray and woman Rabbi try to bring a Catholic and a Jewish family together in a mixed faith wedding ceremony.
Justine and Father Ray must contend with a contend with a condom epidemic at school, and Rachel falls for an ex-convict volunteer worker.
Father Ray receives a call from his friend Father Jesse who informs him that he has contracted AIDS.
Father Leo faces accusation of sexual abuse.