2001
Sonny and Carly renewed their vows in Martinique. Carly plotted with undercover agent Roy DiLucca to free Sonny from the mob by forcing him to turn state's evidence. Sonny broke up with Carly. She hoped to win Sonny back when she believed herself to be pregnant, but it was a false alarm.

2002
Sonny paid Zander Smith to look out for Carly and the two struck up an unlikely friendship. Carly walked in on Sonny in bed with Alexis Davis and after being rebuffed by Zander, she faked her own death. Carly and Sonny reconciled. Alexis was pregnant with Sonny's child but hid the truth from he and Carly.

2003
Carly learned she was pregnant with Sonny's child. Ric Lansing drugged Carly and tricked her into believing they had sex. She fell through the ice at the lake and was rushed to the hospital. Sonny was asked to chose between Carly and their child but both survived. Ric kidnapped Carly and kept her at a panic room at his house, but she was later kidnapped from Ric's home by Alcazar, who developed feelings for her. After Carly returned home, Sonny moved out, fearing for his child's safety and accidentally shot Carly in the head as she gave birth to their baby. Carly survived surgery but began to have sexual fantasies about Alcazar triggered by her brain injury. The couple reconciled but she remained drawn to Alcazar.

2004
Sonny spotted Carly kissing Alcazar when she went to say a final good-bye, and he broke up with her. Alexis confessed to Carly that Kristina is Sonny's daughter, but Carly kept the secret in exchange for Alexis representing her in a custody trial against Sonny. Sonny offered Carly full custody of the boys. Carly broke up with Alcazar and eventually Sonny asked Carly to move back into the penthouse and they reconciled. Carly began to search for her biological father.