Raphael Rivera (Rafe) was born and raised in Chicago by his unwed, teenage mother, Natalia. He'd yet to meet his father, Nick August, who'd left town before Rafe had even been born. Rafe arrived in Springfield in 2007, unaware that his biological father lived there, with his new family, under the name Gus Aitoro. Desperate for money, Rafe mugged Josh Lewis at knifepoint, and was subsequently remanded to juvenile detention. There he met Gus's stepdaughter, Daisy. The teens never formally introduced themselves to each other, and Daisy fondly referred to Rafe only as "vent boy," because they communicated through the vents in their rooms. An immediate attraction formed between them. When Rafe saw a bully harassing her, he created a distraction by yanking a phone from the wall and punching out their teacher, Coop Bradshaw. Days later, a guard caught Rafe stealing candy for Daisy. During the confrontation, Rafe wrested the guard's gun from him. Gus arrived on the scene with his firearm trained on Rafe. Harley begged Gus not to shoot Rafe, and revealed that Rafe was Gus's son.

While Rafe was in jail for taking the gun, Gus made several attempts to bond with his son. A belligerent and confused Rafe punched Gus, but Gus still lobbied for his son's release. Remy found an apartment for Natalia and Rafe; however, Gus insisted that it was in an unsuitable school district. Natalia agreed to let Rafe to live with the Aitoros for a while. Harley and Rafe clashed when she found a syringe in his possession, and accused him of doing drugs. After Harley learned that he was diabetic, she fretted over how to prepare his meals. Rafe was intrigued to learn that Gus was a member of the wealthy Spaulding family. He soon became acquainted with his grandfather, Alan, who shared Rafe's disdain of Harley. When Rick and Alan argued over Beth, Rafe punched Rick.

After Daisy arrived home from detention, Rafe and she pretended that they didn't know each other in front of their parents, but continued their budding relationship in private. Harley discovered that the babysitting money was missing from the cookie jar, and while at the Bauer barbecue, she accused Rafe of taking it. An enraged Rafe stormed home, where Daisy and he made out on the couch. Harley found the kids embracing, and she accused Rafe of accosting Daisy. Daisy tried to explain things, but Rafe ran off in disgust. Later, the adults decided that Rafe and Daisy should not live in the same house, and Daisy moved in with her father.

The teens ran away together, and as their families looked for them, they hid in the Spaulding lake house. While there, Rafe had an insulin attack, and Daisy called Natalia for help. Rafe recovered at the hospital, and the adults fought over where Daisy and Rafe should live. Alan convinced Natalia and Rafe to move in with him to ensure that Rafe got the best medical care for his condition. Against Gus and Harley's advice, they moved into the mansion, and Alan lavished his new housemates with gifts.

Natalia was still adamant that Rafe not see Daisy, and after Natalia rejected Daisy's offer to exchange time with Rafe for time with Gus, Daisy warned Buzz that Natalia wanted Gus. As a result, Buzz told Natalia that her working at Company caused a conflict for his family, and she quit. Rafe assumed that Daisy had gotten Natalia fired, and he broke up with her. They eventually reconciled. Daisy almost got Rafe into trouble when she shoplifted a watch. Rafe quickly called Alan, who saved the day by buying the watch himself. Though Rafe was impressed with how Alan had handled things, Gus was not. Rafe eventually became a candidate for an experimental diabetes treatment. Rafe declined, fearing that Natalia couldn't handle it if the treatment failed.

Gus's marriage to Harley was deteriorating due to Gus's conflicted feelings for Natalia, Dylan's designs on Harley, and Alan's interference. The couple separated, and Rafe encouraged Gus to follow his heart. Before Gus and Harley were to renew their vows, Alan left a fake message for Gus saying that Rafe was sick, causing Gus to miss the ceremony. When Daisy found out, she confronted Alan, and ended up arrested for assaulting Alan's butler, Jeremy. Rafe convinced Jeremy to drop the charges against her.

Weeks later, Rafe and Daisy declared their love for each other, and made love at the lake house. Harley caught them, and their furious parents once again forbade them from seeing each other. Daisy eventually confided in a concerned Rafe that she was in trouble, but would not explain why. Gus and Rafe slowly started to bond, and Rafe contemplated touring Europe at Gus's suggestion. Soon after, Daisy stunned Rafe with the news that she'd had an abortion.

Hurt that Daisy hadn't consulted him about a decision that conflicted with his religion, Rafe reeled into a downward spiral, lashing out at everyone. A drunken Rafe got himself arrested, and Remy and Daisy appealed to him with no avail. Alan bailed Rafe out of jail, and Gus and Natalia tried to help their son come to terms with the abortion issue. After Rafe defended Daisy to obnoxious kids at a student council meeting, she attempted to reconcile their relationship. Daisy tried to explain that she'd gotten an abortion because she hadn't wanted Rafe to resent her for ruining his life. Rafe, however, wasn't ready to forgive Daisy, or make peace with her actions.

As the weeks went by, Daisy got her life back together, but it appeared that Rafe's was falling apart. An angry-at-the-world Rafe started skipping school, and acting out. Alan worsened matters by feeding Rafe's fear that Gus would choose a family with Harley over one with Natalia. When Gus accepted Harley's invitation to Thanksgiving, Natalia got her and Rafe shifts at Towers for the day. While working, Rafe blew up at a customer, who had been rude to his mother. He walked out on the job, got drunk, and crashed Harley's Thanksgiving dinner. Later, Daisy confided in Rafe that she'd felt empty ever since the abortion. Their talk helped, and Rafe finally started softening as he held her.

Natalia and Gus decided to get married, but when Rafe saw Gus kiss Olivia Spencer on the cheek, he questioned his father's loyalties. Gus thought that he was just helping his ailing friend, but in 2008, Olivia's intentions toward Gus became obvious to Rafe and Natalia. Olivia brazenly made a play for Gus's affections, and to prevent Olivia from ruining her wedding day, Natalia locked her in the bathroom at the Bauer cabin. The ceremony was still disrupted when Gus got the message that the hospital had a heart for Olivia, but Olivia was nowhere to be found. Olivia guilted Natalia into letting Olivia have a shot with Gus before she died.

Natalia and Rafe bickered over the decision, and Rafe defiantly grew closer to Daisy. Still intent on marrying Natalia, Gus bought a house for him, Natalia, and Rafe. Daisy and Rafe decided to get an apartment together, and set up a fake ID ring to pay for it. Harley's new live-in boyfriend, Cyrus, put an end to their operation, though he promised not to turn them in. Still angry with Gus, Rafe blew off a meeting with him. That same day, Gus crashed a motorcycle while rushing to the hospital to see a dying Olivia. Gus died in surgery, and despite protests from Rafe; Natalia donated his heart to Olivia. Though Daisy tried to be there for Rafe, he was more concerned about taking care of his mother, and informed Daisy that he would not be moving in with her.

When the student driver involved in Gus's accident claimed on the stand that Gus had run the traffic light, Rafe threatened him, and had to be dragged away by the police. Olivia took advantage of Natalia's economic troubles to force Natalia to sell Olivia the house Gus had bought. Weeks later, Alan confided in Rafe that he'd been having visions of Gus. In Alan's visions, Gus had mentioned the numbers 5-1-2. That same day, Harley gave Rafe some of Gus's things, which included a Cubs jacket. Inside the jacket, Rafe found 512 twenty-dollar bills. Rafe told Olivia about the money, who later suggested that Natalia buy the house from her with that money. Meanwhile, Rafe decided that after graduation, he was going to join the Marines and become a cop. Though Alan tried to dissuade him, Natalia thought that was a wonderful idea.

The day of graduation, Mallet told Rafe that the District Attorney, Jeffrey O'Neill, was about to make a statement that Gus was on the take. Apparently, in exchange for getting Olivia to the top of the transplant list, Gus had let the clients of a certain defense attorney slide. Mallet informed Rafe that although he'd tried to cover up this information, O'Neill conducted his own investigation and was about to go public. Determined to save Gus's reputation, Rafe threatened Jeffrey with Gus's old service revolver. Mallet entered, startling Rafe, and the gun went off, hitting Jeffrey in the chest. Rafe fled to the house that Gus had bought. Daisy found him, and persuaded him to talk to Harley.

Desperate to save Gus's son, Harley fled the country with Rafe. Although Buzz arranged for a worried Natalia to visit Harley and Rafe, when Harley feared that the authorities were on to them, she and Rafe slipped away again. After being on the run for months, Rafe gave Harley the slip, and returned to Springfield. He met Daisy, but their reunion was cut short By Grady Foley, Daisy's new boyfriend. Ducking out before the cops arrived, Rafe went to the boardinghouse to see his mother. Natalia urged Rafe to see Frank Cooper before anyone else on the police force knew he was in town. A reluctant Rafe agreed. While apparently waiting for Frank, Rafe saw the police approaching. Assuming that Natalia set him up, he ran off, and called Daisy. They met at Harley's abandoned house where Rafe asked Daisy to run off with him. Daisy made it clear that she only wanted to be his friend. During their discussion, the police surrounded the place, believing that Rafe had taken Daisy hostage. Realizing that Daisy was in danger, Rafe turned himself in.

Since bail was set so high, Rafe languished in prison until his trial, and Daisy and his mother frequently visited him. Unbeknownst to Rafe, Natalia refused to let Olivia pay for the lawyer, and had resigned herself to giving him sexual favors in return for legal advice; however, Olivia saved Natalia before anything drastic happened. Before Rafe's case went to trial, Buzz Cooper warned Rafe that Natalia might go to extremes to help him. Worried for his mother, Rafe accepted a plea bargain, but despite Jeffrey's call for leniency, a judge sentenced Rafe to two years in prison.

Prison life was not easy, and Rafe tried to shield his mother from the knowledge that he was getting beaten up by fellow prisoners. Though he asked Daisy not to tell his mother, Daisy did. A distressed Natalia confided in Olivia, who ultimately got the governor transfer Rafe to a better prison in exchange for Natalia selling the house that Gus had bought. Several weeks later, Frank got Rafe assigned work in the prison library, if Rafe studied to get his GED. When Frank admitted that he had feelings for Natalia, Rafe encouraged him to date her. Later, around Christmastime, Frank arranged for Rafe to work a prison detail near Company, and Rafe shared a reunion with his mother. At Company, Rafe learned about Natalia's interest in buying Cassie Lewis's old farmhouse, and agreed with Frank that it was a good idea.

Rafe's stint in prison continued into 2009. At one point, Rafe went into shock due to his blood sugar, but recovered. Both Natalia and Olivia rushed to his side; however, when he learned that they'd run out on Emma's school presentation, he told them to return for Emma's sake. Soon after, Rafe was excited to learn that Natalia and Frank were engaged. When Rafe asked if his mother was happy, Natalia strongly implied that she was. Later, Rafe was released from prison early, in thanks he thought, to Frank. Unfortunately, Rafe still had to spend a brief time in a halfway house. Rafe suggested that Frank and Natalia marry before he entered the halfway house. Natalia agreed, but stunned everyone by jilting Frank at the altar. Immediately after, Frank took Rafe to the halfway house. Weeks later, Frank admitted to Rafe that he and Natalia weren't meant to be, but hoped they could stay friends. Months later, Rafe was released from the halfway house after Frank volunteered to act as his mentor.

Rafe tried to follow in Gus's footsteps by enrolling in the police academy, but Frank said that Rafe's prison record would disqualify him for admission. Rafe still deeply resented Olivia after all the pain she'd caused his family. When she stepped up to offer him a job, as mandated by his parole, a belligerent Rafe refused to bus her tables, and told her to butt out of his family. Natalia tried to help Rafe adjust to life outside prison, but he yelled at her for smothering him. He was short tempered with everyone, except Frank. Rafe found Olivia's influence over his mother troubling, but was flabbergasted when he saw Olivia and Natalia stroking each other's faces. Natalia admitted that Olivia and she had become romantically involved, and wanted a family with Rafe and Emma. Rafe rejected the idea, and admonished his mother for betraying her religious beliefs. Rafe moved in with Frank, who eventually admitted that he'd found out the lesbian relationship on the day of the wedding. Frank advised Rafe to try to understand his mother, but Rafe vehemently rejected Natalia and Olivia.

On Independence Day, Rafe saw Olivia milling around, waiting for Natalia, and he berated Olivia for wanting to get with both his father and his mother. Natalia left on a religious retreat without saying goodbye, and Rafe became even more disillusioned with her. Rafe continued to be friends with Daisy and Ashlee. When he realized that Daisy was dating his cousin, James, he told her that it was cool, but warned James not to hurt her. Natalia returned, revealing that she was pregnant, and Rafe took it as a sign from God that Natalia was meant to be with Frank. Even though Natalia said that she intended to raise the baby with Olivia, Rafe taunted Olivia, saying that she'd be alone while Natalia was with Frank.

Weeks later, Rafe decided to enlist in the Army. His mother refused to let him go, but Rafe said that she couldn't expect him to respect her choices, if she didn't respect his. Natalia cried, and worried what might become of him. Alan said that he was proud that a Spaulding would serve their country. The day that Rafe was set to leave, Alan died of cardiac arrest following a bone marrow transplant to save Phillip. Rafe wanted to postpone his deployment, but Buzz said that Alan would want Rafe to go. Rafe left, and returned a year later to meet his new baby sister, Francesca.