Rafe Kovich spent the early days of his life moving between homeless shelters with his mother in her quest to protect Rafe from Caleb Morley, whom she believed to be the king of vampires. Rafe's mother Alison took Rafe to Port Charles but she was murdered shortly after their arrival. Rafe was befriended by Molly Lansing and she welcomed him to town. After Rafe met Molly, he found his mother's body and was a suspect in her murder.

Rafe insisted that he was innocent and Molly stood by her new friend. Molly feared for Rafe's safety after Lucy Coe, a friend of Alison's mother, warned Molly that Rafe was not safe in jail. Meanwhile, Rafe had an encounter with Caleb in which he learned that Caleb was his biological father. Rafe escaped from Caleb but did not believe he would be safe at the police station since Caleb had reached him there. He turned to Molly and she hid him at her home until her mother discovered him and returned him to police custody. Molly and Lucy helped Rafe escape from police custody.

After Rafe escaped, he helped police officer John McBain and Lucy track down Caleb after they learned that he had kidnapped Molly's sister Sam Morgan and her infant son. While they searched for Caleb, they discovered that Caleb's real name was Stephen Clay and that he had suffered a mental break after the death of his wife, a woman that looked like Sam. Rafe cared for the child while Lucy and John saved Sam and killed Caleb in the process. The charges against Rafe were dropped after Caleb was named as Alison's killer.

After the charges against Rafe had been dropped, he was placed in a group home while Lucy made plans to become his legal guardian. However, Lucy's request for guardianship was denied. Molly immediately begged her mother to allow Rafe to stay with them, but Sam took on the role instead. Rafe was extremely grateful to Sam but he struggled to adjust to all the changes his life had undergone in such a short time. Molly remained a good friend to Rafe and his feelings toward Molly became romantic.

Just as Rafe settled in to his new life with Sam and her son, his uncle Silas Clay arrived in Port Charles and petitioned the court for guardianship. Although Silas was a doctor, he did not have a warm bedside manner and Rafe wanted nothing to do with him. Sam planned to fight Silas for guardianship but her good intentions were deterred after Silas diagnosed her son Danny with leukemia. The court sided with Silas but he allowed Rafe to continue to live with Sam until her son's health was stable. Silas remained in town and Rafe got to know his uncle better as Silas saved Danny's life. Afterwards, he willingly moved in with his uncle.

Molly and Rafe became closer during Danny's battle with leukemia and Rafe made his feelings for Molly known. They shared a kiss but Molly told Rafe that she could only offer him friendship because she was in love with her boyfriend T.J. When Molly's boyfriend slept with someone else, a girl named Taylor, Rafe hoped that Molly would change her mind about him. However, Molly chose to remain with T.J. while both Taylor and Rafe were heartbroken. When Taylor suggested that she and Rafe pretend to date in hopes of garnering attention from T.J. and Molly, Rafe agreed.

The fake romance between Rafe and Taylor caused a small amount of tension between Molly and T.J. but it did not break up the couple as Taylor and Rafe had hoped. As Rafe continued to pine for Molly, he overheard a conversation between T.J. and Molly in which T.J. revealed that he had been present during a mob shoot-out. Rafe informed the police, which placed T.J. in danger. When Molly learned what Rafe had done, she re-evaluated her choice to be friends with him. Molly severed their friendship completely after Rafe reported to Molly's mother Alexis that T.J. had booked a hotel room to be with Molly.

After Rafe's friendship with Molly was destroyed, he turned to cocaine. Sam and Silas were unaware of his drug use but Sam noticed that he had an unusually strong reaction to the death of Patrick Drake's infant son. When Sam figured out that Rafe had caused the accident, he made plans to flee town using the funds he had secured from Nina Clay. As Rafe attempted to outrun what he had done, Molly jumped in the car with him and he confessed that he had intentionally driven Patrick's car off the road. Before he was able explain why he had caused the accident, the car crashed into a road block and he was rendered unconscious.

Rafe briefly regained consciousness and tried to talk to Patrick about what he had done. However, his full confession was cut off when he experienced a seizure and required an immediate brain surgery. During the operation performed by Patrick, an artery was hit which rendered Rafe brain dead. While Rafe remained on life support, his family hoped that his life could help another through organ donation but their hopes were dashed when the toxicology report showed that Rafe had used heroin in addition to cocaine. Rafe's friends and family mourned the loss of his life and surrounded him with their love as his life support was turned off.

Weeks after Rafe's death, Victor Cassadine admitted that he had instructed Rafe to cause the car accident which had killed Patrick's son. Victor explained that he had enticed Rafe to do his bidding by offering him hope that his mother could still be alive.