Carly Manning was sunbathing nude on a beach in Tahiti, where she met up with Adrienne and Justin Kiriakis. Carly was on the run and decided to take Justin and Adrienne's advice and hide in Salem. Carly arrived in Salem and was shocked when she saw two people she knew. One was her long lost boarding school friend, Jennifer Horton. The other was Bo Brady, the man who broke up a fight between her and Lawrence years ago. Bo, however, did not remember Carly. Carly and Bo despised each other, yet bonded over Bo's son Shawn Douglas. Shawn Douglas had gone deaf as a result of falling into a pipe at a Jencon Oil site. Carly was the doctor who treated him and she taught him sign language. Carly had learned that her brother, Francois, aka Frankie Brady, was being held by Lawrence and would only be released if he was given the VonLeuschner fortune and Bo Brady. Carly intended to give Lawrence what he wanted, but changed her mind when she began developing feelings for Bo. Later, Carly learned that Jennifer had tried to marry Lawrence in her place and was raped. Carly's disgust for Lawrence became even greater after that and increased when he came to Salem. Carly was relieved that her brother Frankie was safe, but she refused to give Lawrence her family's fortune.
Bo and Carly fell in love, but Bo was still mourning his wife and couldn't make a commitment to her. Carly, who was acting as Victor's physical therapist, accepted his wedding proposal, even though she didn't love him.
Bo befriended a young girl named Emmy Borden, who was in love with him. The night before Carly was to marry Victor Kiriakis, Bo wrote a love letter to Carly begging her not to go through with it. Bo asked Emmy to deliver it to Carly, but unknown to Bo she gave it to Victor. Victor replaced Bo's letter with a forged one that urged Carly to marry Victor. He sent a forged letter from Carly to Bo telling Bo that she was in love with Victor and was going to marry him. Devastated, Bo showed up at their wedding and toasted to them with a glass of champaign. Unfortunately, the champaign he drank was poisoned by Emmy, who expected Carly to drink it. Bo was infected with the virus that Lawrence had created and was using to kill off ISA agents.
Carly married Victor on May 5th, 1991. Because Victor was still paralyzed, Carly and Victor could not consummate their marriage. Carly further held off Victor's advances by claiming it would jeopardize his recovery.
When Victor Kiriakis learned that Bo was infected with Lawrence Alamain's virus, Victor offered to trade the "John Black" file to Lawrence for the cure. The deal fell through and during the trade the vial fell to the floor and broke. Luckily, Carly Manning was able to save some of it and reproduce the cure, saving Bo and many others.
In a last ditch attempt to break up Bo and Carly, Victor faked his death and fled to Mexico to find a set of codacies.
Roman, John, and Marlena all traced their medals to a Mayan temple in Mexico. Roman Brady, Marlena Evans Brady, Isabella Toscano, John Black, Bo Brady, and Carly Manning all went to Mexico in search of the truth. Once in Mexico they found Victor Kiriakis chained in one of the temples. Eventually they made their way to a room in which Stefano DiMera was waiting for them. Using the medals, Stefano gained access to a set of Codacies which promised the holder power beyond imagination. Stefano also held a satchel which held the truth about John's past. Suddenly an earthquake occurred, setting of a volcano, and the temple began to crumble and fill with lava. Stefano threw the satchel into the fire and was then crushed and lost among the falling debris. John managed to recover the satchel, but the contents were badly burned. After Bo and Carly had a symbolic Mayan wedding, everyone headed home.
Bo was kidnapped by the Torres family in 1992 in an attempt to get police commander Roman Brady to ease up on their drug shipments in Salem. Bo was supposed to be traded for a shipment of confiscated drugs, but when Carly Manning blew the trade, a Torres brother dead. Raffi Torres blamed Carly and he set Bo's boat adrift while Shawn D. and Carly were aboard it. Carly and Shawn D. were rescued by Lawrence Alamain and Bo was rescued by Roman. Later, Bo recognized a birthmark on Carly's neck as the birthmark of the mysterious woman John Black had a photograph of. Carly told John she was unsure when the photograph was taken, but she never recalled seeing him before. Carly did however recognize a locket John back from Switzerland and told him that Lawrence had a similar one.
In 1992 Carly began having nightmares about the child she lost many years ago. Carly confiding in Bo about her child. Years ago after Carly had learned that her current lover Charles (I forget the alias Lawrence really used) was really Lawrence Alamain, she fled. Carly learned she was pregnant and went to Vivian Alamain for help. Vivian took care of the pregnant Carly and was there when her child was born. Carly never got to see her child and Vivian and the doctor told Carly that the child was born with water on the brain and would soon die. Haunted by what really happened to her child, Bo and Carly flew to France, where Carly gave birth. After talking with the doctor he admitted to Carly that her child did not die and was sold on the black market. Carly and Bo returned to Salem and Vivian seemed to be as shocked about the development as Carly was. Meanwhile, Lawrence's new lover and attorney, Lisanne Gardner, had also informed Lawrence about Carly's trip. Lawrence went to France to search for answers of his own, but found nothing. Originally Carly had told Lawrence that he wasn't the baby's father, but later she admitted he was but that their baby had died.
Carly and Bo eventually set an official wedding date, but their wedding would never happen. Lawrence soon learned that Nikki was his and Carly Manning's son. Lawrence verbally attacked Vivian, who had a heart attack as a result. Lawrence told Carly about Nikki and the two discussed their options. First they both agreed to protect Nikki from knowing that he had killed Lisanne Gardner. They told Nikki right away that Lawrence was his father, but they didn't tell him Carly was his mother. When Carly and Nikki began to bond, Vivian panicked and tried to flee Salem with Nikki. Lawrence then burst into Bo and Carly's wedding and announced that Vivian had run off with their son Nikki. Bo eventually caught Nikki and Vivian before they could leave the country.
Bo learned the truth about Lisanne's death and Bo and Carly tried to move on. However, when Nikki learned that Carly was his mom he wanted to reunite his parents.
In 1993, Vivian learned that she had been diagnosed with a fatal heart disease. If Vivian could not have Nikki then she didn't want Carly to have him, so she set out to frame Carly for trying to kill her.
Vivian enlisted the aid of Dr. Wu, who gave her some herbs that would make Carly Manning very agitated and angry. Vivian spiked Carly's drinks with them several times in order to provoke her. At an evening at the Penthouse Grill, Vivian agitated Carly out on the terrace and Vivian lept off it. Vivian claimed Carly pushed her, but Victor Kiriakis saw Vivian jump. Not only was Vivian's plan ruined, but she was paralyzed from the waist down as a result. In the hospital, Vivian enlisted Dr. Wu once again for some herbs that would allow her to walk again. Unfortunately, the herbs also made her a tad crazy. Vivian decided to have Carly arrested for putting some of her patients out of their misery. Vivian began injecting Carly's patients with cleaning fluid. Vivian's plan worked and Carly came under suspicion for murdering her patients. When Vivian attempted to kill Caroline Brady, who had suffered another heart attack, Vivian found her and the two fought. Carly ended up falling on the needle and was injected with the cleaning fluid. Carly fell into a coma and the police believed that she was trying to kill Caroline, but ended up injecting herself. Later, Vivian spiked Carly's IV with some herbs which made her appear dead, but she wasn't. Vivian had Carly buried in a special coffin which not only featured some lights and an air tank, but a two way speaker phone on which Vivian could talk to Carly. Eventually Carly's air began to run out. Vivian, who was home from the hospital, was weaned off the herbs she was talking because she was now able to walk on her own. When she realized what she had done, Vivian told Lawrence, who dug Carly up. Lawrence wanted to take Carly to the hospital, but Vivian told her that the hospital could do nothing to her because of the herbs. Vivian called Dr. Wu, who treated Carly. When Carly came to she had no idea who Nikki or Bo was and she believed Lawrence to be James, the man she fell in love with before learning who Lawrence really was. Lawrence attempted to escape with Carly, but Billie found them at the airport and she brought Nikki with her. When Carly saw Nikki, she remembered everything. Vivian was sent to an insane asylum for what she had done. As a side effect, Carly's love for Lawrence resurfaced when she realized how he had become the man she fell in love with, James. Carly, Nikki, and Lawrence all left Salem at the end of 1993.