Carmen Santos entered the picture in 1999 when Michelle was discovered to have been the one who killed Carmen's son, Mick. Carmen wanted her son, Danny, to do away with the murderer, but, instead, he married her to protect her. Disgusted, Carmen did her best to come up with a way to end the marriage, so that she could have her revenge and avenge her son's death. Despite her best efforts, Carmen was unable to break up Danny and Michelle. She also was unable to keep Danny from leaving the family business. Although Carmen hoped to eliminate Michelle's hold on Danny by killing her, her plans failed and all she accomplished was to alienate Danny. Hoping to draw Danny back into the family, Carmen set it up to look like her life was in danger. The plan worked, with a concerned Danny sticking with his mother, determined to find out who tried to kill her. However, when Danny began asking too many questions, Carmen had to think fast and accused her new attorney, Ben Warren, of setting up the shooting that almost killed her. As expected, Danny confronted Ben and swore he'd get proof against him. Ben, knowing that Carmen arranged for the explosion, confronted Carmen, got her confession on tape, and blackmailed her into giving him more power in the mob. Unfortunately, Carmen's plan to reel Danny into the family failed when Michelle gave him proof that Carmen set up the attempt. Disgusted, Danny called Carmen a monster and tried to walk out of her life.

In late June, Carmen came up with another idea to get rid of Michelle, that wouldn't include murder. When Danny and Michelle went to San Cristobel on their honeymoon, they were visited by Alden Heath, an old friend of Danny's who was now the President of the Santos Bank of San Cristobel. After some small talk, Alden offered Michelle a "box of chocolates" as a supposed, "wedding present", personally made by Alden's wife, Antonia. What neither Michelle or Danny realized was that Alden was a plant of Carmen's and the "box of chocolates" actually contained bearer bonds that Carmen tried to get Michelle to smuggle, hoping that Michelle would be arrested. Later, when Danny and Michelle tried to help Jim Lemay get Cassie Layne and the Lewises out of San Cristobel , on the Santos yacht, Michelle opened her "box of chocolates" and discovered the bearer bonds. Just as Danny realized that Michelle was set up by Carmen, the police arrived and arrested Michelle for smuggling. To Carmen's dismay, Danny, Jim and Josh were able to break Michelle out of prison and smuggle her out of the country. While trying to find ways to get rid of Michelle, Carmen's relationship with Ben was heating up. Unfortunately, Carmen was very jealous of Ben's relationship with his newfound daughter, Drew Jacobs, and her mother, Selena Davis. At the same time, Carmen's daughter, Pilar, hated Ben due to his treatment of her boyfriend, Bill Lewis, and decided to get rid of him by setting it up so Carmen would see him trying to "seduce" her. Unfortunately, Pilar's plan worked all too well. When Carmen saw Ben and Pilar in a compromising position, Carmen shot Ben and then tried to frame Michelle for the crime.

As the year 2000 began, Carmen had two obstacles in her plan to frame Michelle. The first was her daughter, Pilar. Consumed with guilt, Pilar wanted to tell the police what happened the night of Ben's death but Carmen was able to appease Pilar for a little while with promises that she would confessed if Michelle were found guilty. However the stress of Michelle's trial became too much for Pilar and she testified in court that her mother shot Ben. Fortunately for Carmen (unfortunately for Michelle), Pilar's testimony was deemed inadmissible in court and she was placed in a mental hospital where Carmen was determined to keep her until she admitted that she was confused about Ben's death. Another obstacle was Vanessa Reardon. When Carmen learned that Vanessa, who was lingering in a coma after a car accident, was the one who actually fired the shot that killed Ben, she decided to poison her to keep her from waking up admitting her role in Ben's death. Carmen's plan worked and Michelle was found guilty of Ben's murder. Carmen finally had Michelle out of her life--but Danny was not about the let her get away with it. Carmen's own children conspired to find the witness Carmen bribed and clear Michelle. Eventually they were able to locate the witness, Ruth, and after ensuring her son's safety they convinced her to admit to the police about lying. At the same time Vanessa, who was hidden away so Carmen couldn't get to her, woke up and gave her statement to the police. Vanessa and Ruth's statements were enough for the police and five months after Ben's murder, Carmen was finally arrested. After a failed escape attempt, Carmen agreed to a deal: in exchange for testifying against Springfield's mob families she would be released and entered into the Witness Protection Program. However, the day she was set to enter the program, Carmen was shot by a rival family. However, Carmen didn't stay dead for long. A mere 5 months later, she resurfaced, determined to get rid of Michelle once and for all. Unwilling to let her hurt Michelle and learning that Carmen had murdered his own father, Danny shot Carmen and dumped her body in the river.

Several months later, in the summer of 2001, Danny and Michelle learned that Carmen wasn't dead after all, but was saved by one of her henchman. When Michelle confronted her, Carmen kidnapped her. Carmen was determined to get rid of Michelle once and for all until Danny found them. Though Danny pleaded with his mother to spare Michelle, she was determined to make Michelle pay for destroying the family. Before she got a chance to carry out her threat, Carmen heard sirens and was forced to flee. Not long after, Carmen unexpectedly showed up at the Bauers with her grandson, Robbie, in her arms. Although Danny and Michelle were certain that she was planning on kidnapping him, she surprised them by announcing that she was ready to turn herself into the police. In jail, Carmen called to speak with FBI agent, Gus Aitoro and offered Gus a deal: she'd turn over the Machados and the Sandovals in exchange for her freedom. Although she scoffed when Gus demanded that she turn over Danny too, she soon relented and disguised herself as a powerful mob boss called "Mr. Big" in an effort to draw out Danny. Although, Danny suspected that Carmen was "Mr. Big" she continually denied it. As the sting went on, Carmen seemed to be setting Danny up, however, in the end, it turned out it was all a ruse. For unbeknownst to Gus, Carmen made a new deal with his superiors--immunity for her in exchange for the other mob families, not Danny. Meanwhile in 2002, Carmen was worming her way back into the family, professionally and personally. Although claiming to have gone legit, Carmen was still involved in smuggling. When too many people, including Danny, began asking questions about her export/import business, Carmen had her henchman, Maurice, destroy the evidence by blowing up the warehouse. Unfortunately, the plan had disastrous results with Danny being trapped in the explosion! Danny recovered but had no memory of what was in the warehouse. Unfortunately for Carmen, Danny's memory soon returned and, although he suspected she was being the fire, he kept quiet, with the knowledge that her fate was now in his hands.

On the personal front, Carmen encouraged Catalina Quesada in her obsessive quest to win her nephew, Tony from Marah Lewis. To Carmen, Tony/Marah were just a younger Danny/Michelle, and one was more than enough for her. When Catalina was murdered, Carmen spearheaded the efforts to clear Tony's name, and this brought her into very close contact with Danny. This did not thrill Michelle, and Carmen exploited this, as well as Danny's inability to shake his mob ties, as often as she could. Although she didn't immediately succeed in breaking up Michelle and Danny, she did play an instrumental role in breaking up Tony and Marah when she ordered Romeo Jones (who had murdered Catalina under Maria Santos's order) to reveal his one-night stand with Marah to Tony. Meanwhile, she also renewed her personal and romantic ties with Edmund Winlsow, as she needed his help in getting a country club membership. She then enlisted Edmund's unwitting help in breaking up Danny and Michelle when she videotaped Danny plotting to kill Edmund. Danny blamed Edmund when the tape was delivered to Michelle, and to retaliate, Edmund made Carmen think she had taken poison. Once that fright was over, Carmen went back to gloating over Danny and Michelle's breakup, this one far more likely to be permanent than their separations in the past. Unfortunately, things did not go as she planned and Danny decided to deal with her once and for all. First, he embezzled a large portion of her money to pay off Cassie Winslow's mob debts. Soon, Danny began working with the FBI to bring Carmen down. She learned of his duplicity before his plan was complete and one night on the cliffs, they struggled over a gun and she shot him in the stomach. He fell, to his presumed death.

Carmen was guilt-ridden. As the days passed and a body was found, Carmen was unnerved. By the time of the funeral she was nearly insane from grief and regret. Soon after the funeral, Carmen went to Danny's mausoleum, and was visited by his spirit (actually a hologram). She confessed her crime, was arrested, and learned Danny had been alive all along. Carmen forgave Danny, but told him he would never be free from his mob ties. Carmen was then sentenced to a lengthy prison term but escaped. On New Year's Eve, she cornered Michelle alone at the Bauer home. Carmen's plan to finish off Michelle once and for all nearly succeeded, but Bill Lewis entered the home, snuck up on Carmen, and jumped her. During the struggle for the gun, Carmen hit her head on the floor. Suffering from severe blood loss, she lapsed into a coma, and was taken to Cedars, where she remains, still comatose.