Ray Santos grew up as part of the Santos crime family, but never became involved in the family business. After the murder of his father, Frederico, whose dead body was found in a river in Chicago, and the death of his mother two years later, Ray and his younger brother, Tony were raised by their uncle. As an adult, Ray would join the priesthood to get away from the life of the mob and was ordained as a Catholic Priest in Springfield in 1999.

Although not directly involved in the family business, Ray always remained close to his family, sharing a special closeness with his cousin Danny. When Danny was reluctant to get involved with Michelle Bauer, Ray encouraged him to follow his heart. Soon Ray's influence and support helped Danny to leave the family business and pursue a life with the woman he loved, so Ray performed Danny and Michelle's second wedding in a private ceremony at Laurel Falls. Not long after, Ben Warren was murdered and, in 2000 when Ray's cousin, Pilar, came to him to hear her confession, Ray happily obliged. What he didn't expect was for her to tell him that her mother, Carmen, had shot and killed Ben! Though at this time, Michelle had been falsely accused of the crime, Ray was unable to break his vow, and was forced to remain silent, hoping that somehow Michelle would be cleared. As time went on, Pilar grew more and more emotionally distraught. Ray eventually took her in and let her live at the rectory with him until things settled down.

During Michelle's trial, Pilar finally confessed all in the courtroom. Unfortunately, she was found to be incompetent and her testimony was disregarded. As Pilar was sent away to the psychiatric ward at Cedars, Michelle was found guilty of Ben's murder and sent to prison. While she awaited sentencing, Ray visited Michelle in prison and let it slip that he had known the truth all along. Michelle was angry, but forgave him when she came to the conclusion that his testimony wouldn't have helped her case anyway. Facing the possibility of the death penalty, Michelle went along with Danny when he decided to break her out of prison. On the run and completely alone, the young lovers sought Ray's help. Reluctant at first, Ray tried to get them to turn themselves in. When Danny reminded him that he owed them for not speaking up about Pilar's confession, Ray gave in and agreed to help. He disguised the pair as a priest and a nun so they could escape to San Cristobel. To Ray's delight, Carmen was finally exposed as the murderer and Michelle was cleared of all charges.

Not long after, Ray was accidentally shot when Tony, fleeing from trouble in Chicago, arrived in Springfield. At first resentful of Ray's advice, since he felt that Ray became a priest simply to run away from the family, Tony surprised Ray by going to him when he had a moral dilemma about whether to kill Danny in order to head the family business. Ray urged Tony to do the right thing and be loyal to Danny and Tony ultimately decided against taking Danny's life. Soon Ray would become Tony's confidant since Tony felt that he gave pretty good advice for a priest. In addition to giving Tony advice about his relationship with Marah Lewis, Ray, knowing they were meant for each other, also kept after Danny and Michelle to reconcile after they separated.

In 2001, Ray befriended Catalina Quesada and helped her to get a job at Infierno and fought against his growing feelings for her. Later, a distraught Catalina informed Ray that she was pregnant with Tony's baby and implied that she was considering an abortion. Not realizing that he was playing right into her hand, Ray told Tony that Cat was pregnant. Despite Ray's reservations, Tony decided to marry Cat for the sake of the child. In 2002, Cat confessed to Ray that she'd miscarried the child but lied about it. Ray was disgusted by what she had become and though he urged her to tell Tony the truth, Cat refused and reminded Ray that he couldn't disclose what she confessed. Not willing to let the matter drop, Ray informed Tony that he couldn't marry the couple and said that Cat knew the reason. Thinking that his refusal to perform the wedding would force Cat to tell the truth, Ray was shocked when, instead, she lied that Ray had been sexually harassing her. Tony didn't believe her, while Ray, wanting to get everything out into the open, brought in the Bishop and asked Cat to repeat the charge against him. When a reluctant Catalina refused, the Bishop sent Ray to a retreat yet told him he had nothing to worry about.

Not long after, Marah went to Ray with her suspicions about Cat's pregnancy. Though he refused to tell her anything, later when Tony found him, he realized that he could tell him about Marah's suspicion. Furious, Tony went to confront Cat only to find her lifeless body. That day, Tony was arrested for murder. Confused at his unwillingness to say anything in his defense, Ray offered to hear Tony's confession. When he refused, Ray realized that Tony was innocent and was covering for someone. Later, when Marah asked questions about Cat's death and Romeo Jones, Ray suspected that Romeo was the real killer. Confronting Tony, who believed that Marah was the murderer, the brothers realized that Marah was in danger and Tony broke out of jail to save her. To Ray's delight, Romeo was finally arrested and Tony cleared of all charges.

Later, Ray tried to help Tony deal with his attempted rape of Marah, as well as Danny's marital rift with Michelle. Later, Danny was apparently killed by Carmen who confessed her crime to Ray, expecting absolution. Even at harm to his personal safety and beliefs, he refused to forgive her latest acts of violence. To Ray's delight, Carmen was soon hauled off to jail and Danny, who returned alive, together with Tony,moved away from the mob into a more legitimate business. Unfortunately, in 2003, Ray came to suspect that perhaps Danny wasn't as legitimate as he claimed, although Danny would not confirm his suspicions. That fall, Ray was on hand to defend Nico Castaņa, a young street kid who was apprehended for mugging Michelle. Though Danny wanted to press charges, Ray explained to Danny and Michelle that Nico's parents were killed a few years earlier in the crossfire during a mob hit instigated by the Santos family and that Nico was essentially a good kid. Though Danny felt losing his parents was no excuse for criminal behavior, Michelle realized that Santos family was responsible for Nico's circumstances, and taking Ray's word that Nico was a good kid, she refused to press charges. Not only that, she offered to let Nico to stay with her and Danny.

In 2004, Father Ray happened upon a conflicted Billy Lewis who was contemplating ending his years of sobriety by taking a drink. Sensing that Billy needed to talk, Ray counseled him by telling him that talking about his troubles would be preferable to drinking them away. Although Billy didn't confide his troubles to Ray, he did leave the bar without taking that drink. That summer, Ray supported Danny when Michelle was caught in a warehouse explosion and ended up with amnesia. Later, when Danny confessed to Ray his responsibility in causing Michelle's accident (he was working undercover to bring down the mob and used the explosion to fake a mob hit) Ray urged him to overcome his guilt and just love Michelle. He also warned Danny that the old Michelle could be gone forever, so their duty was to accept her for who she was now. Not long after, Tony, the only person Michelle found any connection to, confessed to Ray that he had a sexy dream about him and Michelle. Ray tried to assure his brother that the dream might not have to be taken so literally.

Unfortunately, the results of that dream would ultimately lead to tragedy in 2005. Despite Ray's warnings that when Michelle's memory returned she'd go back to Danny, Tony found himself falling for her. The feeling seemed to be mutual with Michelle and Danny planning to divorce. Although Ray tried to convince everyone to take things slowly since there was a chance that everything could change should Michelle's memory happen to return, no one would listen. Eventually, Tony and Michelle became engaged, a situation that did not enthuse Ray since he knew Tony would get hurt. Unfortunately what Ray feared would happen, happened with horrible consequences. Michelle's memory returned and although she tried to go through with marrying Tony, she was forced to confess to him that she loved Danny. Enraged, Tony attacked Danny and the two slipped from a cliff. Although Michelle grabbed hold of them both, the weight was too much and Tony let go in an effort to keep Michelle from falling along with them. Several months later, Ray was pleased to officiate a newly reunited Danny and Michelle's wedding.

In 2006, Ray was called to administer last rites to a dying Reva Lewis. At peace with her condition, Reva asked him to say a prayer with her so that her family will find peace. In early 2007, Ray officiated at the wedding of Jonathan Randall and Tammy Winslow. However, things ended tragically with Tammy's death in a hit and run and Ray was forced to administer last rites to the young woman mere days after her wedding. A devastated Jonathan, in denial, tried to stop Ray from performing Last Rites, and then begged for him to ask God to save Tammy. Unfortunately, it wasn't to be. Several months later, a friend from Chicago asked Ray to check on Natalia Rivera and her teenage son, Rafe. Apparently, the two belonged to his church but had recently moved to Springfield. Weeks after meeting Ray, Natalia asked him to speak to her son whose girlfriend had just had an abortion without his knowledge. Though Ray tried to reach out to the boy, Rafe rudely dismissed him. Weeks later, Gus Aitoro and his wife, Harley, went to Ray to discuss getting an annulment. After explaining exactly what an annulment meant in the church he gave them the necessary paperwork but asked them to think about what they were doing before they signed it.In 2008, Ray was again there when people needed his support-- this time mainly Reva and especially Natalia.

In 2009, Ray was pleased to learn that Natalia had gotten engaged to Frank. When Natalia questioned her feelings, Ray urged her to listen to her heart. Though Ray intended to officiate the wedding, he was called away the last minute. Later, he learned that Natalia ran out and left Frank at the altar. Weeks later, Natalia confided in Ray that she had feelings for someone else. From the way that Natalia looked at Olivia Spencer's picture, it didn't take long to realize who it was. While Ray tried to argue that, according to Scripture, her feelings were wrong, Natalia argued her belief that God had no issue with whom she loved. Weeks later, when Natalia confessed that she was pregnant with Frank's baby, Ray suggested that she go on a retreat so that she could sort through her feelings. That same day, Ray enjoyed a pleasant visit with Danny and Michelle. At summer's end, Michelle and Danny decided to move back to Springfield. At about this time, Ray officiated the double wedding of Billy Lewis to Vanessa Chamberlain and Buzz Cooper to Lillian Raines.