Joseph "Joe" Scully, Jr., grew up in Bensonhurst, New York with Sonny Corinthos and Sonny's girlfriend Connie Falconeri. Joe was named after his father notorious organized crime boss Joseph Scully, Sr. While Joe and Sonny were teenagers, Joe Sr. employed Sonny in his organization and he favored Sonny over his son as the heir to his business. Joe left Bensonhurst to run a strip club in Atlantic City but went underground after he experienced troubles there.

Several years later in the summer of 2012, Llanview police detective John McBain and Sonny separately tracked Joe down in New Orleans. John McBain wanted to find Joe because he believed that Joe had killed his sister years ago in Atlantic City. Sonny wanted to find Joe after his girlfriend Kate Howard (Connie Falconeri legally changed her name) claimed that Joe had raped her as a teenager and a pregnancy had resulted from the rape.

Sonny arranged for Joe to be brought to him in Port Charles and he confronted Joe at gunpoint over what he had done to Kate. Joe claimed that Kate had thrown herself at him and that she was not a person to trust since she had abandoned their child at birth. While the men argued about Kate, John arrived and accused Joe of murdering his sister Theresa when she had worked at Joe's club in Atlantic City. Joe admitted that he had killed Theresa after he caught her talking to a federal agent. John was the man she had spoken to and Joe told John that Theresa's death was on his hands.

Joe was taken into police custody and held in Atlantic City. While in lock-up, he received a visit from his son Trey Mitchell. Joe reassured his son that the charges against him were false and that Sonny was to blame. He warned his son to his real identity as Joe Scully, III secret from Sonny. Trey wondered why his father had agreed to provide the financial backing for Trey's production of the reality show Mob Princess which featured Sonny's daughter Kristina. Joe explained that after he was unable to discourage Trey from doing the show, the next best idea would be for Trey to hide from Sonny in plain sight.

While Joe remained in lock-up he devised a new plan to maintain his son's safety and gain leverage over Sonny after Trey admitted that Kristina had a romantic interest in him. Joe instructed his son to marry Kristina so they could regain what Sonny had taken from them. Trey disliked the plan but agreed to move forward with Kristina in order to help his father. Joe also turned to Johnny Zacchara for assistance in his plight against Sonny and reminded Johnny that the Scully family and Anthony Zacchara had been allies. However, Johnny refused to get involved.

Joe also contacted Jerry Jacks for help with is legal battle. Jerry agreed in exchange for Joe's assistance with his current operation. Joe hesitated briefly after he admitted that it would be difficult to find manpower for Jerry since most of the people Joe had supplied Jerry with for the Metro Court robbery had been killed on the job. Regardless, Joe agreed to work with Jerry again.

Trey remained distant from his father and Joe moved forward with his plan to take down Sonny without Trey's assistance. He kidnapped Kristina on the day of Sonny's wedding to Kate and took her to Sonny's warehouse. Joe tied Kristina up and explained that he was Trey's father and that he planned to kill her as punishment for everything that Sonny had taken from the Scully family.

Kristina pleaded with Joe for her life and warned that him that her father would avenge any harm that came to her. Joe reminded Kristina that her father was occupied at his wedding but the day he married Kate would forever by marred by Kristina's death. As Joe prepared to pull the trigger Trey entered and stepped in front of Kristina to protect her. Joe tried to convince his son that Kristina's death would bring them everything they had ever wanted and instructed him to move out of the way. Trey insisted that he had a wonderful life and that he cared for Kristina. Trey made a move to take the gun away from Joe and as the men struggled for the gun a shot was fired into Joe's shoulder.

Trey was concerned for his father but Joe ran off. He arrived at Tracy's home with a gunshot wound and claimed that Sonny had his men attack him but he escaped. Tracy moved to call the police but Joe insisted that police involvement would make things worse. He also refused medical attention but asked Tracy to tend to his wound instead. She removed the bullet and afterwards a police officer arrived and asked if Tracy had seen Joe While the two spoke, Joe used the opportunity to escape.

Joe found refuge with "Duke Lavery," unaware that the man was actually Cesar Faison disguised as Duke. It was revealed that "Duke" was behind the plan for Trey to marry Kristina. "Duke" had arranged for Sonny's assets to be transferred to Kristina and then Trey would inherit everything of Sonny's upon Kristina's death. "Duke" was disappointed with Joe's inability to murder Kristina but informed Joe that another plan was already in place to take everything away from Sonny. The first role Joe had in the new scheme was to shoot Sonny's accountant, Bernie Abrahms. Joe fired a shot into Bernie but Jason Morgan arrived and fired his own shot into Joe before he was able to shoot Bernie again.

Jason tended to Bernie and Joe used the opportunity to sneak away. He was badly wounded from the gunshot but he made his way to the Quartermaine mansion and sought refuge there one final time. Tracy offered to call an ambulance but Joe realized he was dying and turned down the offer. Instead, he asked Tracy to call his son. She initially refused until Joe admitted that he had saved her life when Jerry Jacks had poisoned the town's water supply. Once Trey arrived, Joe told him in Tracy's presence that Sonny had shot him. Joe died after he named Sonny as his killer.