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.