After the Joe team was shut down, Scarlett and Snake-Eyes were engaged to be married, and retired to a house in Georgia. During that time, Snake-Eyes agreed to train the young woman named Ophelia to be the last student of the Arashikage clan. She was to undergo her final trial, but Snake-Eyes continued her training, which began to worry Scarlett. She didn't know that Snake-Eyes was planning to go on one final commando mission to train Ophelia. Duke, now working covert ops, asked Snake-Eyes to join a mission to capture Firefly. Only a week before his planned marraige to Scarlett, Snake-Eyes went on the mission without telling Scarlett, believing she wouldn't approve. The mission turned sour and a number of soldiers involved -- including Ophelia -- were killed. She had been his apprentice, but she also reminded him of his late sister, and her death devastated him. He didn't return to Scarlett for a week, and the day of their wedding came and went. When he finally arrived in Georgia, Snake-Eyes and Scarlett spoke briefly, but the damage was done and their engagement was ended. Snake-Eyes retreated to the seclusion of his mountain cabin while Scarlett tried to move on with her life. She did not see Snake-Eyes for years.

    In 2001, the G.I. Joe Team was reinstated by the government in reponse to Cobra's return to the United States. Duke brought many of the older Joes to help train and lead a batch of new recruits and Scarlett is now one of the team's highest ranking field commanders. Snake-Eyes is also a member of the new team. At first, Scarlett maintained a necessary working relationship with Snake-Eyes, but she had not yet forgiven him and barely acknowledged him when off duty. After the couple was captured by Cobra during the nano-mite incident, they reconciled with each other while facing their possible deaths. They were again engaged to be married, but continued to work with the Joe team.

    Scarlett's many missions for the new team have included battling mutated soldiers in the arctic, rescuing Flint and the Baroness from Russian mobsters, stopping Tyler Wingfield's terrorist plot and battling against a revived Serpentor on Cobra Island. She later joined Snake-Eyes on a mission to seek out Cobra Commander, who was hiding in a Red Ninja retreat in Tibet. Snake-Eyes had sent fellow ninja T'jbang into the retreat on an unauthorized mission there, and he needed to be rescued. This angered Hawk who put Scarlett in charge of the mission in lieu of Snake-Eyes after making it clear he was not happy. On that mission, Snake-Eyes defeated the leader of the ninjas who then pledged their loyalty to him. This turn of events upset Hawk even further. Scarlett came to her fiancee's defense, but Hawk placed them both on probation for their next mission fighting Cobra troops in Badhikstan. Before they could reconcile with their commander, Hawk was shot by Cobra Commander and was left paralyzed in a hospital bed. In Hawk's absense the Jugglers took the opportunity to take control. Snake-Eyes and several other Joes were arrested, while the Jugglers cut down the team's roster to about a dozen members. They also placed General Philip Rey in command of the team. After Duke's subsequent arrest, he and Snake-Eyes were rescued by Scarlett and Storm Shadow, who revealed he had finally broken free of Cobra's mind control and asked for Snake-Eyes' help. Scarlett advised them both that they should try once more to reconcile, but if they couldn't, they should end their relationship once and for all.

    Rey, Duke and the remaining Joes fought Cobra Commander's plans to unleash the deadly superweapon known as the Tempest. At the same time, the Joes faced a new threat in the group called the Red Shadows, who had begun targeting and murdering Joe and Cobra agents. The Red Shadows also sparked violence and instability around the globe, hoping to take control of the world. When the Red Shadows attempted to kill Hawk, Scarlett helped rescue him as she and Snake-Eyes returned to the team to help in their plans to defeat both Cobra and the Red Shadows. The battle with the new organization became shockingly personal when while attempting to save her husband Flint from a Red Shadows agent, Lady Jaye was killed. Scarlett was the first Joe to come upon the terrible scene. In the end, Duke, Hawk and Rey's small team defeated the schemes of the Red Shadows and Cobra. Shortly after these threats were neutralized, the G.I. Joe team was again disbanded by the military.

    One year later, the Joe team was reformed with a smaller roster of active members, including Scarlett, Snake-Eyes and Storm Shadow, under the command of Joe Colton. When two orbiting satellites crashed to the Earth in Chicago and Silicon Valley, killing thousands, the new Joe team mobilized to discover who was causing the crashes. Colton allowed some members of the team to investigate independently, though some assumed the disaster was the work of Cobra. Scarlett headed to Massachusetts to track down former Cobra agent Cesspool. She snuck into his home late at night to discover him in bed, dying from cancer thanks to the toxins he had been exposed to years earlier. His wife then appeared and a fight ensued between her and Scarlett. The Joe won the fight, and was met by whom she thought were the Cesspool's children, but were in fact disguised robots who captured Scarlett. She was soon brought to Destro and held onboard his submarine headquarters. Destro's son, Alexander, thought having Scarlett there was dangerous and tried to free her. Destro discovered this and argued while Scarlett pretended to remain unconscious. She eventually escaped, just as the Joe team arrived. Using Scarlett's microscopic tracking device -- she and Snake-Eyes had them implanted to keep track of one another in an emergency -- they had found her location and went on an unauthorized rescue mission. During the mission, to stop the sub from flooding and killing the others, Snake-Eyes locked its blast doors from the inside as Storm Shadow watched in dismay. When the Joes were able to get inside they found Snake-Eyes' lifeless body. By all indications Snake-Eyes was truly dead. As a devastated Scarlett grieved, the body was somehow stolen. Scarlett's grief turned to anger as the Joes attempted to track down his body. They were all shocked to discover that the Red Ninjas, led by Sei Tin had not only stolen his body, but they had miraculously revived him. But Snake-Eyes had been brainwashed by the ninjas to be used as a weapon. Scarlett and other Joes were captured by the ninjas and Scarlett pleaded with Snake-Eyes to try and break free of the mind control. Eventually, Storm Shadow fought his old friend, and was being beaten until he threatened Scarlett's life, hoping to bring his friend's mind back to the surface. He eventually succeeded, and the Joes freed the Red Ninjas from their new leader's influence.

    When Snake-Eyes returned to the team, he revealed to Scarlett that the Baroness was being held prisoner there according to Storm Shadow, and while Colton knew she was there, he kept it from the rest of the team. After Stalker was informed, the three Joes confronted Colton, very wary of all the past betrayals from high-ranking officers. Colton told them he had his orders to keep the incarceration quiet, and they had no right to know. They were interrupted by a sudden power outage. A military commando team named the Phoenix Guard lead by General Rey had arrived with orders to take control of The Rock. A battle followed and Scarlett, Colton and others hid from the attackers, hoping to get out a call for help. Rey was under orders from the president's chief of staff, Garret Freedlowe, but it soon became evident that unbeknownst to Rey, his team was made up of disguised Cobra agents. When Colton finally contacted the president, he learned that Freedlowe had been replaced some time ago by Cobra Commander. The Joes defeated the infiltrators, but not before they had killed many members of the base's support staff and the Baroness escaped. Just after that incident, a small team of Joes including Scarlett was rushed to shut down Cobra's illegal oil-drilling operation in the arctic. After that mission, the Joe team took some time off to regroup and recover from the assault on The Rock. Scarlett and Snake-Eyes went on leave separately; her to visit her family in Atlanta and Snake-Eyes to his mountain retreat.