Johnny was introduced to the Salem scene as part of Ernesto Toscano's plan to destroy Victor and recover Loretta's diary. Ernesto had kidnapped Bo, and hired a plastic surgeon to alter the faces of Bo Brady and a renegade ISA agent, Johnny Corelli, so that Corelli could infiltrate Salem and do Ernesto's dirty work. Bo not only managed to convince Johnny not to go through with it, he also convinced the plastic surgeon to tell Ernesto that it had been done, so Bo was released and sent back to Salem, with Ernesto believing it was actually Johnny. Johnny escaped and also went to Salem.

Shortly after arriving in Salem, Johnny got himself involved with Victor Kiriakis, and became yet another one of his lackeys. He hooked up with his brother, Nick, but it soon became a case of sibling rivalry when they both began fighting for the love of the same woman, April Ramírez. When Nick was murdered at the Jencon plant on Halloween night, Johnny was one of the prime suspects (along with Victor Kiriakis and April Ramírez). Johnny's harassment of Whitney Baker, a police psychiatrist, did not help much, as Roman became more convinced than ever that Johnny was guilty. Johnny could have cleared himself when the police began suspecting Justin Kiriakis, who admitted to arguing with Nick that night, but he chose to step forward and testify that he saw Justin leaving the refinery while Nick was still alive.

With the investigation at a standstill yet again, Tanner Scofield came forward and claimed to have seen Eve Donovan at the refinery that night, leading to her arrest. Roman soon discovered that Tanner had lied, because he was also being harassed by Johnny (Tanner was also a patient of Whitney Baker's).

Unfortunately, he couldn't prove it. When a number of Salemnites boarded a train they had heard carried the gun that killed Nick Corelli, Johnny hired a man named Harry Hill to sabotage it, and he eventually detached the car from the rest of the train. Roman was finally able to prove there was a connection between Harry and Johnny when Isabella revealed that Johnny made a number of calls to Harry from her private phone line.

Johnny finally admitted that he had harassed Whitney and Tanner and hired Harry, but swore he did not kill his brother. Roman sent him to jail anyway, but soon realized that if Johnny didn't do it, he had to be protecting somebody. Roman figured out that the killer could be only one person...April Ramírez, the woman whom Johnny and Nick had both loved, and who was Johnny's only friend in Salem. When questioned, April admitted that she had been there that night, that she had seen Nick, and that she had even pointed a gun at him, but she didn't kill him...Jo Johnson was the one who had killed him, seeking revenge for Nick because she believed he was responsible for her son Steve's death.

Although April and Johnny had been running Wings together and growing closer, realizing the depths of Johnny's illegal activities eventually drove April out of his life. She couldn't deal with the fact that he was involved in so many dirty deals. She left Salem and went to New York. Johnny Corelli floated around for awhile before eventually leaving Salem, although he did do one good thing with the time he had left in that town...he had located Anjelica Deveraux and her son, Alexander, and convinced Anjelica that Alexander would be better off with his father, Justin, and stepmother Adrienne. He brought the boy back to Salem and returned him to his delighted father, who had thought his son was dead.