When Sonny tried to end his marriage, Lily told him she was pregnant. Brenda knew she had lost him. Brenda moved on by marrying a widower, Jasper Jacks. However, the marriage proved to be invalid when Jax's previous wife, Miranda, turned out to be alive.
Lily was killed in a car explosion, but Brenda remained with Jax. After she was kidnapped to draw Sonny into a trap, she and Sonny were trapped together in a cave. They expressed their feelings and made love which Brenda later admitted to Jax.
Brenda was ecstatic when Sonny asked her to marry him and leave Port Charles and the mob behind. On their wedding day, Brenda walked down the aisle with no groom at the end. Sonny, believing he could not protect her, sent Jason Morgan to the church to tell Brenda that he had left without her. Brenda was deeply hurt and hated Jason for agreeing to do this for Sonny.
She moved back in with the Quartermaines for a period and then lived with Jax as friends while he helped her deal with Sonny's betrayal. Brenda's mental state deteriorated and she was institutionalized. She regained her strength and decided she wanted to be with Jax, not Sonny. She and Jax planned to marry, and upon Sonny's return, he realized she had moved on. When Brenda's mother, Veronica, showed up in Port Charles, Brenda was tested for a hereditary mental illness that Veronica had. Veronica drove Brenda and herself over a cliff, and they were presumed dead. After Brenda's "death," Jax burned the test results without reading them.
When Jason left Sonny's accountant to watch her, Brenda escaped and went to Jax's wedding to Skye Quartermaine. Jax was shocked to see Brenda, who warned him about Alcazar's plan. Alcazar was able to find them and shoot Jax.
Jax survived and Sonny arrived and shot Alcazar. He explained to Brenda that he faked his death in order to get to Alcazar. Jax was paralyzed, and Brenda decided to help him in his recovery while telling his new wife that she was dying and would not interfere with their marriage. However, Jax and Brenda grew closer, and Skye discovered that Brenda did not have her mother's fatal mental illness.
Brenda became worried about her closeness with Jax and blackmailed Jason into marrying her. Jason agreed only to prevent Brenda from reuniting with Sonny, who was married to Carly. Alcazar, who also survived his bullet wound, convinced Skye to help him kidnap Brenda. He took Brenda away on a plane with Sonny hidden onboard. The plane crashed and they all survived but were stranded in the jungle. Jason and Carly rescued Sonny and Brenda, and Jax discovered Alcazar's lie. Jax left Skye because she kept the truth about Brenda's illness and he soon found Brenda to tell her she was not dying and profess his love for her.
When Alcazar was murdered, an angry Skye lied that Brenda killed him. Jason and Brenda were arrested, and although Jax attempted to take the fall, charges against him were dropped. Although Brenda and Jason constantly bickered and fought, they decided not to get an annulment so that they would not be forced to testify against each other during the murder trial.
Jax wanted Brenda to flee, but she refused to let Jason face the charges alone. When seemingly damning evidence surfaced against Brenda, she pleaded with Jason to leave the country with her, but they ultimately decided to stay. New evidence kept Brenda and Jason from being convicted and sent to jail. Brenda and Jason left the country to have their marriage annulled, however, she convinced Jason to get the annulment back in Port Charles where it would take longer because she was not ready to marry Jax.
When she felt she was ready, Brenda and Jason, with a new understanding of each other, had their marriage annulled. Brenda ran into Sonny on the docks the night before her wedding to Jax. She forgave him for leaving her at the altar years before and told him she understood why before they shared a steamy goodbye kiss.
Sonny's wife Carly witnessed the kiss. At the altar with Jax the next day, he responded "I don't" when prompted by the priest to say "I do." Brenda was confused, but Jax explained that he knew about her kiss and that he did not trust her not to cheat on him with Sonny. Brenda ran into Sonny after Jax left her and told him of her breakup. He revealed that Carly had also left him. Upon returning to his penthouse, Jason found a crying Brenda with all her things packed. She decided to leave Port Charles and Jason took her to the airport.
Before Jason left her there, Brenda told him that he deserved to be happy more than anyone she knew. While waiting alone for her flight, Brenda reminisced with a smile about her time with Sonny and Jax. In late 2007, after a nasty fight with Carly, Jax disappeared to Europe. Carly did some snooping and discovered that Jax had flown to Rome to see Brenda.
Jason and Brenda arrive in town on September 30, 2010. On October 8, 2010, Brenda visits Jax's and they talk about how things are doing for them.
In the middle of 2011, Brenda is caught up between the custody battle of Jax and Carly. Jax wants her to testify about how dangerous Sonny's world is and if she did, she would be going against Sonny and Carly. Brenda testifies about the incident of the shooting that happened earlier, but also states that Sonny is a good father. This strains her relationship with Sonny greatly. Jax is set up by Sonny and Brenda is devastated by this. She decides to leaves for Rome with her son Alec. Jax flies them in his private jet on July 21, 2011.
In 2013, she also came to see Sonny because she has moved on too. She reveals to a visibly livid Sonny that she is engaged to Jax.
At Brenda and Jax's hotel room at the Metro Court, Carly tells Jax that Brenda was at Sonny's. Brenda has to admit that she was with Sonny last night and wanted to know if there is still a possibility of getting back together. Jax walks out on Brenda. Brenda shows up at the Nurses Ball to honor Robin, and walks into the Metro Court on the red carpet, much to Carly and Sonny's surprise. Carly takes a few digs at Brenda on live television, but Brenda casually brushes her off and says her (and Jax, in spirit) are there in Robin's honor.
In the ballroom, Brenda finds her name card next to Jax's. Carly comes over with the signed divorce papers and goads Brenda into an argument. Brenda exclaims that Carly is jealous and an "enormous bitch." Sonny and Shawn intervene, and they take their seats for the Ball. Later, Brenda begins a food fight and Carly kicks her out. Brenda decides to head back to Rome.