Johnny was a troubled man who had suffered extreme psychological abuse at the hands of his ruthless and mentally unstable father, mob boss Anthony Zacchara. During one of Anthony's infamous fits of rage, Anthony aimed a gun at his young son with the intention of murdering Johnny, but Johnny's mother jumped into the path of the bullet at the last moment. Johnny watched his mother die as Anthony blamed Johnny for Maria's death. Johnny's beloved older sister, Claudia, whisked Johnny away before Anthony could harm his young son. After Maria's death was covered up, Anthony punished Johnny for Maria's murder by sending Claudia to Italy to live with her uncle, Rudy. Johnny eventually became Anthony's new obsession, as Anthony's mind continued to unravel.

As Johnny grew older, he acted out by running away and getting into trouble. One night, he picked up a hitchhiker, who turned out to be Lulu Spencer. Lulu had just had her heart broken when she learned that her boyfriend had cheated on her. Feeling upset and angry, Lulu had begun walking and accepted a ride from a stranger. Johnny and Lulu ended up stranded and took shelter in a barn while people were frantically searching for Lulu. Concern for Lulu mounted as everyone realized whom she had ended up with.

Trevor continued to be frustrated with Johnny's lack of compliance when Johnny refused to follow Trevor's orders to work with Jerry Jacks. Both Trevor and Jerry wanted to put Johnny in his place so Trevor had Jerry kidnap Lulu. Johnny worked with Jason to rescue Lulu and then Johnny made a statement of his own when he blew up a Zacchara ship. Johnny was injured in the explosion but he knew Trevor and Jerry would be after him. Johnny went into hiding at the Haunted Star. Lulu found him and helped him recover from his injuries. Lulu and Johnny slept together after he recovered, but Lulu remained determined not to enter into a relationship with Johnny because he was too reckless and dangerous.

Since Trevor was unable to control Johnny, he decided replace Johnny at the helm of the organization. Trevor arranged for Johnny's half-sister, Claudia, to move from Italy to Port Charles. Trevor believed she would be easy to control. Johnny was thrilled to have his older sister in town, and Johnny enjoyed watching his sister disagree with Trevor.

When Sonny's girlfriend, Kate Howard, was shot, Sonny believed Johnny was behind the shooting and held Johnny hostage at an asylum. When Johnny was released, he and Claudia vowed to kill Sonny. While they developed a plan to kill Sonny, Johnny invested in the Haunted Star as a silent partner as a means to get closer to Lulu.

Claudia informed Johnny she had made arrangements for Sonny to be killed. Johnny needed his whereabouts to be witnessed, and Lulu became his alibi. They were at the Haunted Star when the hit on Sonny was carried out. The bullet meant for Sonny ricocheted, and his son Michael was shot in the head. Lulu knew Sonny would accuse Johnny of shooting Michael, so she went to see Sonny to convince him of Johnny's innocence. When she arrived at Sonny's, she walked in on Johnny holding a gun on Sonny. Lulu was disturbed by what she saw and swore she was done with Johnny.

Ric Lansing secured Anthony's release from prison. Anthony was disappointed when Johnny wanted nothing to do with him. Anthony decided to use Lulu as leverage over Johnny, but Lulu wanted nothing to do with Johnny. Anthony threatened Lulu's family and coerced her into dating Johnny again. Johnny and Lulu entered into a pretend relationship until Lulu admitted she wanted to date Johnny. Despite her relationship with Johnny, Lulu's ex-boyfriend, Logan Hayes, continued to pursue her.

Johnny and Claudia tried to get away from Anthony, and they moved in together to an apartment across from the Metro Court Hotel. Anthony still arranged for Johnny's release after Johnny was arrested for assaulting Logan. Just after Johnny was released, Lulu was waiting for Johnny at his apartment, and she witnessed Logan attack Maxie at the Crimson office. Logan saw Lulu watching him from Johnny's apartment, and Logan went after her. Lulu stabbed him to death. Johnny arrived after Lulu killed Logan, and Claudia arrived soon after. Johnny told Claudia he had killed Logan to protect Lulu. Claudia and Johnny dumped Logan's body and attempted to cover up the crime.

Lulu knew Johnny would be the main suspect in Logan's death, and she agreed to let Johnny cover for what she had done on one condition: Johnny needed to go on the run with her. Johnny was arrested for Logan's murder, and when Lulu went to visit him, she carried in a gun. Johnny used the gun to take Lulu hostage, and they escaped. Johnny took Lulu to his former piano teacher's apartment in New York. They went by the names Joe and Linda. Johnny posed as a piano teacher and gave lessons to the landlord's daughter in exchange for rent. While Lulu and Johnny were in New York, Lulu's mental health began to decline. She had visions of Logan and was confused about what was real. Johnny took Lulu to Shadybrook for treatment, and he was arrested.

At Johnny's trial, Claudia testified that Johnny had killed Logan when Johnny walked in on Logan trying to rape her. Trevor paid off a juror to ensure Johnny was found not guilty. When Lulu was released from Shadybrook, Johnny and Lulu continued their relationship.

Johnny left the family business when Anthony made Sonny the head of the family. Anthony required Claudia and Sonny to marry to make the transition of power official. Johnny was disgusted his father would marry off Claudia, and he was disappointed in Claudia for going through with the wedding. Johnny struggled to find a job, and Anthony tried to force Johnny to depend on the family by setting him up for assault charges. Anthony's plan did not work. Instead, Lulu and her father intervened to get Johnny released.

Johnny felt he was not good enough for Lulu when he was not able to find a job. He lied to Lulu when he told her he had been hired as an orderly at the hospital. Johnny shared with Maxie that he did not believe he was good enough for Lulu. Maxie agreed that she felt the same way in her relationship with Spinelli and then Maxie and Johnny kissed. They admitted they had a mutual attraction, but they each wanted to try to make their relationships work. Johnny offered to drive Maxie home, and they found Robin's minivan on the side of the road during a winter storm. They found Robin and her daughter, Emma, in the snow and took them Mercy Hospital. General Hospital was unsafe because a deadly bio-toxin had been released. When Maxie learned Spinelli was inside General Hospital, she went in after him, but Johnny pulled her out. After the crisis, both Lulu and Spinelli questioned why Maxie and Johnny had been together, so Maxie and Johnny created a cover story.

When Johnny still could not find a job, he opened his own garage. He was upset when Lulu tried to drum up business for him. Johnny also took a job escorting Maxie to Crimson events. He continued to be drawn to Maxie, and he kissed her again. Johnny used Maxie to push Lulu away when the secret of Michael's shooting was close to being revealed. Johnny told Lulu he was interested in Maxie, and Lulu broke up with him.

While drinking at Jake's, Johnny met an attractive older woman named Olivia Falconeri. They slept together and planned for the encounter to be a one-time occurrence, but they enjoyed each other's company and continued sleeping together. Both Olivia and Johnny agreed they were only interested in a casual fling. When Claudia learned of their affair, she tried to pressure Olivia into staying away from Johnny, but Olivia refused. Sonny also advised Olivia against any involvement with Johnny, and Sonny made a play for Olivia. She rebuffed Sonny's advances and remained with Johnny.

Johnny kept his distance from Claudia during her marriage to Sonny. Johnny did not understand why Claudia wanted to remain married to Sonny with the knowledge that at any time Sonny could learn about her involvement in Michael's shooting and kill her. Johnny tried several times to convince Claudia to return to Europe, but she refused. Johnny did not support Claudia's scheme to become pregnant with Sonny's child, but Johnny was by Claudia's side when she lost her baby after she was involved in a car accident. Claudia believed Michael was responsible for the car accident that had caused her to lose her baby. Johnny disowned Claudia when he realized she had sent Jerry Jacks to kill Michael.

Anthony continued to plot against Sonny, and he was concerned that Johnny could get caught in the crossfire when he went after Sonny, so he arranged for Johnny to be kidnapped. Johnny escaped and learned Claudia was gone. Sonny had planned an elaborate birthday party for Claudia and then used the event to publicly humiliate her and expose what she had done. She disappeared shortly after. Johnny wanted to know what had happened to Claudia, and he wanted Sonny to be punished for the pain he had caused Claudia while she was alive.

Johnny overheard a conversation between Dominic, a member of Sonny's organization, and Olivia. He learned Dominic was actually Dante, Olivia's son with Sonny. Dante was working undercover in Sonny's organization. Although Johnny was disappointed Olivia had not trusted him with the truth, he appreciated the irony of Sonny's own son working to take him down. Johnny worked with Dante to find out what had happened to Claudia, and he showed Dante the mysterious pictures that were being sent to him. The pictures were of Claudia's dead body.

The pictures of Claudia prompted Johnny to reclaim his role as the heir of the Zacchara Organization, and he vowed to avenge her death. Johnny hired Ethan Lovett, and they broke the truce between the Corinthos and Zacchara families when they hijacked one of Sonny's shipments. Johnny tried to impress Olivia with his newfound wealth, but she refused to accept his gifts. He also purchased a penthouse and invited her to move in. Olivia refused because she did not want to ruin what they had.

Sonny was on trial for Claudia's murder, and when Johnny took the stand, he testified that Sonny had been abusive to Claudia. When Johnny learned Michael had killed Claudia, he still wanted revenge against Sonny because Sonny had pushed Claudia to become a desperate and broken woman.

After Johnny's testimony at Sonny's trial, his daughter Kristina wanted to know more about how Sonny had abused Claudia. When Kristina concocted a plan to pretend to date Johnny to upset her father, Johnny went along with it. Olivia was against Johnny using Kristina to hurt Sonny, so Olivia broke up with Johnny. He responded by telling Kristina it was time to end their ruse because they had achieved their goal of unnerving Sonny. He also admitted he loved Olivia. Johnny planned to drive Kristina home when his car exploded. He was able to protect Kristina from the car bomb, and no one was hurt. Johnny guessed Sonny was behind the car bomb, but he was unable to prove it.

The tensions between Sonny and Johnny escalated, and Michael tried to broker a peace deal between the two families. While Michael and Johnny spoke, a car opened fire on them, and Michael pushed Johnny out of the way.

Johnny believed once again that Sonny had tried to kill him. Johnny went after Sonny and pulled a gun on him. When Sonny saw the gun, he shot Johnny in the chest. Detective Ronnie Dimestico was the first to arrive on the scene, and he disposed of Johnny's gun. It appeared that Sonny had shot an unarmed man. As Johnny recovered from the shooting, Jason brokered a truce between the two families, so that they could deal with a new threat. A European mobster named the Balkan had moved to Port Charles. However, Johnny continued to cause problems for Sonny and Jason when he unwittingly hired himself out to men whom he later discovered worked for the Balkan.

Johnny's life took an unexpected turn when Dr. Lisa Niles passed off a syringe that was filled with a deadly toxin, which she had tried to inject into Robin Scorpio's I.V. Johnny quickly hid the syringe before the doctors chasing Lisa caught up to her. Johnny decided to hang on to the syringe as leverage to force Lisa to be a mob physician. One day, Lisa was treating Johnny for a gunshot wound, which he had sustained when he had killed one of the Balkan's henchmen who had been about to talk to Jason, when Olivia walked in. Olivia figured out Johnny had been shot again. Olivia ended things with Johnny for good when she realized he was never going to change his dangerous way of life.

The relationship between Lisa and Johnny began over blackmail, but as Johnny spent time with Lisa, he saw many similarities between Lisa and Claudia. When Patrick and Robin tried to warn Johnny that Lisa was mentally unstable, Johnny defended Lisa. Johnny also denied Patrick's accusations that Lisa had passed the syringe to him and he had used it to blackmail Lisa for medical treatment. Johnny explained to Lisa it was too late to save his sister from her obsession with Sonny, but he could still save Lisa from her obsession with Patrick. Lisa and Johnny began sleeping together, and Johnny tried to convince Lisa she could have a better life without Patrick.

Johnny realized that Robin and Patrick knew that he had the syringe, so he set up a scavenger hunt with clues all over town for Robin and Lisa to find. Robin located the syringe, but she put it in her locker at work when Jake Webber arrived at the hospital in critical condition, following a hit-and-run accident. Lisa managed to steal the syringe out of the locker and then destroy it before Robin could turn it over to the authorities. Johnny hoped that Lisa would finally move forward, but Lisa's determination to destroy Robin only intensified. He washed his hands of Lisa when she tried to kill Robin and frame Patrick for the murder.

Shortly afterwards, Anthony was released from prison. Anthony moved in with Johnny and then quickly began causing problems for his son. Johnny reluctantly agreed to help Lisa one last time by arranging for her to leave the country after she managed to escape from custody. Meanwhile, Anthony had agreed to hide Lisa at a safe house so that she could make one last deadly stand by taking Robin, Patrick, and several others hostage at the hospital. The hostage crisis resulted in Spinelli getting shot and Lisa fighting for her life in a permanent coma after she injected herself with drain cleaner.

Johnny returned his focus to mob business. He offered Michael Corinthos a job with the Zacchara organization in the hopes that they would be able to prevent a mob war from breaking out. Michael decided to take a job with ELQ instead because Michael didn't trust Anthony. Johnny remained unaware that his father continued to plot Sonny's downfall behind Johnny's back.