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, a.k.a 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 champagne. Unfortunately, the champagne 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 5, 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 codices. 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 codices 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 confided in Bo about her child. Years ago after Carly had learned that her beloved James 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 leaped off. 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, with Carly having re-embraced her old life, and her old name.
In October 2009, Carly and Lawrence got into a bad fight. Carly proclaimed that Lawrence was not the man that she married and then stabbed him in the stomach. Lawrence fell to the floor saying "You'll never find..." Carly headed home to Salem in hopes that some of her old friends would help her. She found Bo, who was separated from Hope, and confided in him. The two old-flames soon rekindled their relationship.
Carly had been keeping the secret that she had a brief affair with Daniel Jonas, which produced a daughter - Melanie Layton. When Lawrence found out about the affair, he threatened to kill Melanie unless Carly gave the baby up. So, Carly never told Melanie or Daniel about the pregnancy.
She found both Daniel and Melanie living in Salem. While she instantly connected with Daniel, Melanie and Carly clashed. Carly tried to form a friendly connection to Melanie, but Melanie was not pleased with Carly's interference in her life.
Vivian was also not pleased with Carly. Vivian was out to get revenge on Carly for killing Lawrence, so Vivian decided to carry out Lawrence's original plan and kill Carly's daughter.
On Philip and Melanie's wedding day, Vivian lured Melanie up to the roof. Carly followed and pulled a gun on Vivian to stop her. Just as Carly fired the shot, Melanie stepped in front of Vivian to protect her. Carly was devastated that she had shot her own daughter. When Melanie recovered, Carly told Melanie the truth. Carly was Melanie's mother and Daniel was Melanie's father.
Melanie was furious with Carly for a while, knowing that Carly had given Melanie up to be raised by Trent. Bo tried to comfort Carly as best he could. Eventually, Melanie and Carly worked things out. Carly even smoothed things over with Daniel, who was happily engaged to Chloe.
However, one night Carly learned that Chloe had cheated on Daniel. She didn't know with whom (it was Philip) but Carly ordered Chloe to tell Daniel the truth. Just as she was about to tell Daniel, Chloe found out that she was pregnant. Already depriving Daniel of raising one child, Carly wrestled with the idea of doing it again. Carly agreed to have a paternity test set up for Chloe. If the baby was Daniel's, Carly would keep quiet about Chloe's one-night-stand.
The test results showed that Daniel was the father. Carly kept quiet and even started to form a friendship with Chloe. Chloe and Daniel were married and Chloe soon gave birth to a healthy baby boy, Parker. However, at Parker's baptism, Caroline Brady confessed that she had switched the paternity test results. Philip was the real father. Carly was furious to discover that Chloe had an affair with Melanie's husband. Daniel and Melanie left Chloe and Philip, respectively. They were both angry with Carly for keeping Chloe's affair a secret.
Carly tried to work things out with Daniel and Melanie. Eventually, the three of them began spending more time together. As Carly's family grew closer, her relationship with Bo began to suffer. Hope was arrested for a string of robberies and assaults and sent to prison. While in jail, Hope discovered an organ trafficking scheme. She worked with Bo to expose the secret. When it became clear that Hope's life was in danger, Bo left to help Hope escape from jail. The two went on the run. Carly knew that Bo had made his choice to go back to Hope. As soon as they returned to Salem, Carly let Bo go. Melanie and Daniel were there to comfort Carly.
Carly threw herself into her work. Bo was back with Hope. Daniel had started dating Jennifer. And, her son, Nicholas refused to speak to Carly. Feeling as though she was all alone, Carly began taking prescription pills. She soon became an addict and even stole from the hospital supply. Jennifer found out about Carly's addiction and broke up with Daniel, in hopes that Daniel and Carly would reconnect and Carly would stop using. Jennifer's plan didn't work. Daniel did not have any feelings other than friendship for Carly. Hurt by his rejection, Carly went on a drug binge.
By this time, Vivian found out that Carly had been abusing prescription pills and enlisted Quinn's help to make sure that one of his dealers gave Carly a stash of pills. Then, Vivian set it up so that Carly would see Jennifer and Daniel together, hoping it would drive Carly to go on a drug binge. Vivian's plan worked. Vivian impersonated a maid and entered Carly's room. Vivian gave Carly even more pills and then took a picture of the strung-out Carly surrounded by even more pills. Vivian uploaded the picture and sent it out to everyone in town.
Jennifer was worried about Carly, so she went to the Salem in to find her. Jennifer found a passed out Carly on the floor and immediately took her into the shower, turned on the cold water, and stuck soap in Carly's mouth, trying to force Carly to vomit. Jennifer convinced Carly that she needed to get professional help.
When a picture of a passed-out Carly surrounded by pills showed up online, Daniel went to find her. Daniel found Jennifer at Carly's hotel room. Jennifer confessed that she had known about the pills all along. Daniel was furious with Jennifer for keeping Carly's addiction a secret. While Daniel and Jennifer were arguing, Carly slipped out the bathroom window. Daniel, Jennifer, and Melanie began looking for her. The soon went to the police and Bo and Hope joined in on the investigation.
Carly stumbled through the alleys of Salem. She dug through the dumpster to find almost emptied bottles of beer and drank them. Then, she passed out on the ground. A homeless man came upon her and tried to rape her. Quinn showed up and pulled the man off Carly. Then, he took Carly back to his hotel room to get her off the streets. Quinn had no idea that the woman he was helping was Carly Manning, his mother's sworn nemesis. Despite learning who she was, Quinn still convinced Carly to return to her family and enter treatment.
Carly entered Salem Oaks Rehabilitation facility. There, she went through several intense therapy sessions, including family sessions with Melanie and Nicholas. Carly's doctor forced Carly to deal with the past crimes and misdeed she'd committed - killing Nicholas's father and giving Melanie away. In turn, both children could then truly be able to forgive their mother. Once given a clean bill of health, Carly left for a trip through Europe with Nicholas. Melanie made plans to visit them once she had some time off from work.