A few years after the Joe team was shut down, Flint and Lady Jaye were married and made a home in Fort Meade, Maryland, not far from the Pentagon. At that time, Flint began working on a book about his experiences on the Joe team. 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 Flint became the team's executive officer. Lady Jaye is one of the team's field commanders. Joes have noted that his marraige and new administrative duties have helped Flint tone down his occasional arrogant behavior. After helping to fight Cobra's nano-mite threat and taking part in other operations, Flint was kidnapped by Russian mobsters while on his way to his own book, signing. Both he and the Baroness were being held in the Czech Republic by groups of gangsters hoping to stop Cobra from stealing away their members. The two escaped even as the Joes and Destro joined forces to rescue them, and worked together closely. Once they were rescued, the Baroness -- just causing trouble for the fun of it -- made sure everyone saw her thank him with a kiss. Lady Jaye was not amused and again gave Flint a punch in the mouth before he could explain. Flint later joined the Joes' invasion of Cobra Island to battle the forces of a revived Serpentor.

    Flint found himself in conflict with Duke after his old teammate launched a secret operation in Sierra Gordo. The small nation's new president contacted Duke after Destro offered his services to the country to help them fight a group of invaders who were secretly Destro's Iron Grenadiers. A team of Joes were sent in to assist Sierra Gordo's army in the battle, but Duke had not told them that he was setting up Destro to be captured. In fact, he hadn't told Hawk, Flint or any other Joe what he was planning. Duke personally captured Destro, and two Joes were injured in the fighting. After the operation, Duke faced angry teammates, including Hawk and Flint, who were even considering throwing him off the team for unnecessarily endangering troops. Their argument nearly came to blows before Hawk could separate them. Before the two old friends patched up their differences, the Joe team baited Cobra Commander into a trap by making him believe Destro was onboard a train guarded by the Joes. Destro helped set the trap in exchange for his freedom. In the battle that followed, Hawk was shot and paralyzed by Cobra Commander, who was in turn captured by the Joes. In Hawk's absence, Duke took control of the team, while Flint continued his role as executive officer. The Joe commanders soon found themselves fighting the cabal of generals known as the Jugglers. During this time, Flint and Lady Jaye's relationship became strained as they wondered if they could ever live a normal, peaceful life again.

    With Destro once again free and in command of Cobra, the Jugglers began cracking down on the Joes, intent on reigning in the team or disbanding it all together. Meanwhile, Hawk was seemingly despondent and unwilling to retake command. Duke and Flint did their best to keep the team together with the help of General Joe Colton, though the Jugglers cut down their roster to about a dozen Joes and arrested a number of them. They also placed General Philip Rey in command of the team. Rey, Flint 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. They sparked violence and instability around the globe, hoping to take control of the world. The battle with this new organization became shockingly personal when Flint was attacked by an agent of the Red Shadows and would have been killed if not for the intervention of Lady Jaye. While attempting to save her husband, Lady Jaye was killed as Flint looked on in horror. Devastated and angry, Flint threw himself into the mission at hand while hoping to exact vengeance on the Red Shadows. He nearly got himself killed by infiltrating the Shadows' base on his own before the remaining Joes arrived. Flint nearly shot and killed an unarmed Eden, but was not disturbed enough to turn himself into a murderer. In the end, Duke, Rey and Flint's small team of Joes 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.

    The defeat of the Red Shadows did little to help Flint deal with his grief over Lady Jaye's death. One year later, the Joe team was reformed with a smaller roster of active members, including Flint. Still bitter and angry after Lady Jaye's death, Flint became more aggressive and reckless as the Joes tried to stop Vance Wingfield from crashing orbiting satellites into populated areas. The team's new commander, Joe Colton, expressed his doubts about Flint being a part of the team to Stalker, who convinced the General to keep his old teammate on duty. As Wingfield's threat ended, Snake-Eyes was apparently killed in action. Flint was little comfort to Scarlett in her grief, telling her that the pain only gets worse. After Snake-Eyes was miraculously revived by the Red Ninjas and freed from their control, Flint officially resigned from the G.I. Joe team with little explanation. The team was unaware Flint went on a personal mission to track down the Red Shadows' Wilder Vaughn and bring him to justice. When he finally found Vaughn in Ho Chi Minh City, Vietnam, he witnessed a meeting between Vaughn and the Baroness, who had recently escaped the Joe team's custody. When the meeting ended, though he found the decision difficult to make, Flint followed the Baroness and contacted Joe headquarters that he had found her. Flint followed her to Cobra Commander's hidden base in Honduras, where she hoped to find her kidnapped baby son. As the Baroness met with the Commander and Destro (the baby's father), Flint, Spirit and Snake-Eyes raided the base but were captured. As the Joes watched, Destro turned his company, MARS, over to Cobra Commander in exchange for baby Eugen. Flint and the Joes tried to capture the Commander, but decided against it after the Commander revealed he had learned the names and locations of their family members when he had infiltrated the White House a short time before.

    To help deal with Cobra Commander's growing threat, the Joe team expanded its roster of active members and welcomed Flint back to the team. By this time, while Flint had not completely moved past the death of Lady Jaye, he had moved beyond the anger and seemed more like his old self. The Joes began tracking down as many former and current Cobra operatives as they could find. The team began tracking down as many former and current Cobra operatives as they could find. In Dagestan, Flint helped prevent the assassination of a local official and faced a number of Cobra operatives. G.I. Joe soon learned that the new spike in Cobra activity was part of Cobra Commander's plan to literally start World War III, leading General Colton to activate all reserve members of the team. The conflict spread across the globe as Flint and the core members of the team took the lead in fighting Cobra and the Iron Grenadiers. Eventually, the Joes crushed Cobra and finally arrested Cobra Commander, bringing an end to the war. Most reserve Joes have returned to their previous assignments while Flint continues on as an active member of G.I. Joe