Rafael "Rafe" Hernandez is the handsome FBI agent who was assigned to guard Sami Brady when she was sent into the witness protection program. The two immediately butted heads; but a sweet friendship followed, and they began to fall in love. Rafe learned Sami was pregnant with EJ's child, but kept the paternity a secret out of respect for her.
When Sami and her newborn daughter Grace got out of witness protection, Rafe decided to maintain his relationship with them. He reconnected with his estranged sister Arianna, who objected to his relationship with Sami. Rafe disregarded Arianna's protests and began the process of adopting Grace. Before the adoption proceedings could conclude however, baby Grace died of bacterial meningitis.
Rafe found out that Nicole's baby Sydney was in fact Sami's baby. He helped Sami reunite with her biological child, but their happiness was short-lived, as Sydney was later kidnapped. After EJ helped recover Sydney, Rafe was determined to prove it was in fact EJ who orchestrated the entire kidnapping.
Finally, Rafe got the proof he needed and interrupted Sami and EJ's wedding. A hurt Sami was devastated to hear she had been duped by EJ, yet again. Rafe welcomed Sami back with open arms, and the two spent the night together. Rafe proposed to Sami and she accepted; what he didn't know was that she had snuck out in the middle of the night and gone back to the DiMera mansion to confront EJ. She shot him in the head and threw the gun in the river.
Bo questioned Sami about the shooting, and Rafe insisted she had been with him all night. He believed it, until Sami confessed the truth. Rafe quit the FBI and vowed to protect Sami at all costs. He even rushed their marriage so that he wouldn't have to testify against her if she was arrested. Before they could tie the knot, however, EJ discovered that Sami was the one who shot him. He blackmailed her into giving him sole custody of Johnny and Sydney or he would turn her - as well as accessories Rafe and Will - over to the police. Rafe encouraged Sami to get married that night so they would have one last happy memory as a family. Furious, EJ interrupted and took the children, but Sami went on with the service, and she and Rafe were married on November 24, 2010.
Rafe joined the Salem P.D. and began to investigate EJ, hoping he could dig up some dirt that would help Sami get her kids back. Before his investigation could go very far, Johnny was diagnosed with cancer. Johnny's health crisis prompted EJ to change his mind, and he offered to share custody.
When Rafe was hospitalized after a car accident, Stefano and EJ were ready. They had already created a doppelganger, a petty criminal they had given plastic surgery and trained in all things Rafe and Sami. They switched this double with the real Rafe. Rafe2's job was to break up Sami and Rafe. He even went so far as to sleep with another woman, so Sami would think Rafe was cheating on her. Sami decided to take a break.
The real Rafe was being held prisoner in the DiMera basement. When he refused to give the DiMeras any more information, Stefano injected him with a memory-erasing drug and sent him to live in an institution. Rafe escaped and made his way back to Salem and the safe house where he had first met Sami. There, he came face-to-face with Sami and Rafe2! Sami realized who was who and helped the real article tie up Rafe2 and lock him in the bathroom. Unfortunately, Rafe had no memory and asked Sami who he was. Sami fed him details of their life together, and he regained his memory. They moved Rafe2 to an abandoned warehouse and tried to get him to implicate the DiMeras, but he wouldn't.
Bo and Hope eventually found Rafe2, and Sami and the real Rafe told them the truth. The four took Rafe2 to the DiMera mansion, where he finally confessed that he had killed Fay. Bo and Hope managed to strike a deal with him to testify against EJ and Stefano, but before he could, he was attacked and killed by fellow prisoners who mistook him for the real Rafe. The DiMeras didn't go to jail, but EJ did sign over full custody of the kids to Sami. Rafe and Sami settled into their life together and happily attended the dedication of the new Horton Town Square.
Sami was thrilled to see Carrie, Austin, Marlena and John but amidst the celebration, Rafe got a call from the FBI. He had to arrest John - immediately - on embezzlement charges. Rafe believed John was really innocent and worked to prove it. When he learned of a possible witness who could clear John, he tipped off Carrie - John's lawyer. When Roman learned what Rafe had done, he was forced to fire him.
Carrie felt responsible for Rafe losing his job and convinced her firm to hire him as a private investigator and assign him to John's case. Carrie and Rafe were working together, which caused some discomfort at home for both as they were at odds with their spouses over their belief in John's innocence. Both Sami and Austin wondered if John's brain could still be under Stefano's control.
Things got worse for Sami and Rafe when Johnny went missing after an assassination attempt on John. Sami partially blamed Rafe, as he had convinced her to go to John's party in the first place. Sami went to confront EJ, and while she was at the mansion, they heard an erroneous report that Johnny was dead. Overcome with grief, the two had sex. Sami returned home to find that Rafe and Will had found Johnny. She was overcome with guilt and demanded that she and Rafe renew their vows. They did so on Christmas Eve in front of Tom and Alice's plaque in the town square.
Rafe re-examined the evidence against John and realized that one of the photos had been doctored. He and Carrie brought the evidence to Bo and Hope, who in turn took it to Stefano. He told them he didn't "have access" to the information they needed. Rafe figured out that those words meant John couldn't have had Internet access at the time the funds were embezzled. John was freed!
Rafe and Carrie went into business together. When they solved their first paid case, they were so excited they came together in a kiss. Unfortunately, Sami walked in on this! Irate, and suffering from her own guilt over her indiscretion with EJ, she kicked Rafe out of the loft. He tried desperately to get Sami back, while stuffing his very real feelings for her sister. That is, until he overheard Will confess to Sonny that he had seen his mother and EJ that night. Rafe confronted Sami, then EJ. Rafe and Sami's relationship was over, as was EJ and Nicole's.
Rafe began a very unlikely friendship with Nicole, who was trying to hide her pregnancy from the baby's father, EJ. He even went so far as to "admit" that the baby is his, which seemed to have put an end to any chance he had of starting a relationship with Carrie. After she learned she was pregnant, Carrie and Austin moved back to Switzerland, but not before Carrie told Rafe things might not be as over with Sami as he thought.
When Sami went on the run with EJ, Rafe tracked her down to the safe house. While there, old feelings started to resurface. When they returned to Salem, those feelings were still there, but would they act on them?
