Without telling her husband Jax, Brenda joined with Sonny to unearth clues in his mysterious attack. Sonny's mission was impeded by Detective Taggert of the Port Charles Police Department, who had an unsinkable obsession to bring Sonny Corinthos down. While hiding in the closet, Sonny's claustrophobia returned. He revealed to Brenda that his step-father, Deke, had locked him in closets when he was a child.

During their investigation, Sonny and Brenda grew closer than they had been in months. Despite her marriage to Jax, Brenda continued to find ways to be with Sonny. Sonny realized that he could fully love Brenda while still wearing his wedding ring, so he buried the ring at Lily's grave site. The emotional moment brought closure to the painful chapter of his recent past. A mystery man dug up the wedding ring. Threatening notes, ominous warnings and mysterious gifts began arriving for Brenda at her penthouse.

Arriving home, Jax found Sonny guarding Brenda, who was receiving more threats. The culprit turned out to be Sonny's former friend and confidante, Harry Silver, who, in his fragile emotional state, plotted to kill Sonny and Brenda because he blamed them for Lily's death. It was revealed that Harry, in cahoots with his partner Dr. Pierce Dorman, was behind the drug influx in Port Charles and the heroin injection that nearly killed Sonny.

Harry kidnapped Brenda, who went through a painful withdrawal from her addiction to pain pills. Harry vengefully planned to kill Brenda in front of Sonny. Making her write a "Dear Jax" letter, Harry whisked Brenda away to the catacombs and had her call Sonny. Jax, erroneously believing that Sonny and Brenda had run off together, turned to Miranda for comfort. Hurting and vulnerable, he kissed her, but Miranda retreated from further passion, not wanting Jax on the rebound.

After sustaining a fatal bullet wound while grappling with Sonny, a dying Harry detonated an explosion that sealed Sonny and Brenda in the catacombs, and doomed them to die in each other's arms. Believing they were going to die and realizing that all they had left was each other, Sonny and Brenda made love. Upon their rescue, a guilt-ridden Brenda made Sonny swear that he wouldn't breathe a word of their lovemaking. A pained Sonny watched as Brenda and Jax reunited. In the aftermath, Brenda sought professional help to come to grips with her drug problem. With the help of Dr. Kevin Collins, Brenda decided she needed space - away from both her men - to come to work through her physical and emotional dependencies.

Meanwhile, the Tin Man realized that Sonny and Brenda were on the trail to find who was behind Dorman's murder and the drug trade. Sonny and Brenda soon discovered that it was Rivera who had been the mastermind. Apparently Rivera has not died as Sonny had thought, but was ill and wheelchair bound. Rivera blamed Sonny for the death of his daughter Lily and wanted to kill Brenda for revenge.

Meanwhile, Jax learned that Brenda had escaped jail and he and his newfound friend, Officer V Androwski, tried to look for her and Sonny. They managed to track Sonny and Brenda down and helped free them from Rivera. Sonny wound up shooting Rivera dead and tracked down the Tin Man only to see him sink into the quicksand of the Florida swamps. Brenda and Jax discovered a library of video tapes in which Rivera admitted that he had Dorman killed and was responsible for the drug trade in Port Charles. The evidence cleared Brenda and made Dorman's name mud. The fallout over Dorman made it possible for Monica to clear her reputation and return to her duties at the hospital.

When they returned to Port Charles, Brenda accepted Sonny's marriage proposal. Sonny told Brenda that the only way for them to be safe was for him to leave the mob and for them to leave Port Charles without a trace. Brenda was hesitant to leave her friends in Port Charles, but agreed to Sonny's plan. The Tin Man, however, had survived the quicksand and returned to Port Charles where he died in a final showdown with Sonny. Sonny's ordeal with the Tin Man made him have a dream in which Brenda, instead of Lily had died in a car explosion . This made Sonny realize that he could never keep Brenda safe. With that in mind, Sonny told Jason that he was going to leave the mob and Port Charles, but without Brenda. Sonny realized that the only way he could pull off his plan would be to get Brenda to hate him enough not to follow him. Sonny decided to publicly humiliate Brenda by leaving her at the altar.

Meanwhile, life radically changed for Jason. Jason was now the man in control of Sonny's empire, but he did not want anyone to know. Word had leaked out that Sonny was gone and one of Sonny's enemies tried to kill Jason during a welcome home party at Luke's. Jason, Luke and their guests survived the reign of gunfire, but Nikolas wound up being a victim of mob violence. Jason and Luke helped save Nikolas's life and rushed him to General Hospital.