Shortly after the Joe team was shut down officially, Duke joined Hawk and a small group of Joes for one last mission to deliver an important piece of equipment to a government installation. Chased across the country, Duke and the others lost the device and had to track it down at Cobra's castle in Trans-Carpathia. Some time later, Cobra forces in Europe were defeated by regular military forces and its high command scattered. Following that mission, Duke seemed to leave the Army and "disappear". In reality, he began working classified "black ops" for a secret government agency. A number of his missions for the group involved tracking down former members of Cobra, all fugitives since the group was dissolved. He worked with his former teammate Chuckles when the undercover agent had arranged a meeting with the mercenary Firefly. The former Cobra agent was brokering an arms deal with Chuckles' alias to supply a mysterious employer with weapons. Duke and Chuckles took charge of a top secret military unit known as the Hammer Team on a mission to capture Firefly. The team included former Russian commando Mikhail Derenko, and Sean Collins -- the son of former Crimson Guardsman Wade Collins. It was believed that one of the Hammer Team was a traitor and Duke hoped to force the traitor to reveal himself by secretly including semi-retired Snake-Eyes in the mission, hoping that his appearance would force the traitor to change his plans. The mission proved to be a disaster when Firefly realized what was happening and detonated a number of explosions that killed most of the Hammer Team. While making his escape, Firefly killed Snake-Eyes' young apprentice, Ophelia. Duke would regret his actions during that mission for years to come.

     While Sean Collins took time off from the Army and began his ninja training under Snake-Eyes, Duke and Chuckles continued to try and capture Firefly. They discovered that Hammer Team member Mikhail Derenko had not died a year earlier and had been the traitor on the team. He was now trying to round up former Cobra agents for a new organization, and Firefly was working for him. Duke contacted Storm Shadow, who was still recovering from the brainwashing he received at the hands of Cobra Commander. He allowed Firefly to find the ninja and try to recruit him for Derenko's group. The operation backfired when Snake-Eyes, Sean Collins, Jinx and Budo interrupted seeking revenge against Firefly. Duke and Chuckles were forced to reveal themselves to save Sean and Snake-Eyes. Snake-Eyes and the others were angered by the admission, but Duke convinced them to help he and Chuckles stop Firefly and Derenko from accessing a secret Cobra vault containing information about a secret weapon. The former Joes foiled the plot, though Firefly and Derenko both escaped. Weeks later, after Sean Collins completed his ninja training and took the name Kamakura, Duke recruited him to work for his organization. On another operation for the group, Duke was sent to an arctic research station and fought a group of mutated soldiers who had been involved in a lab accident. Many of his team members were either killed or were transformed into monstrous creatures. Duke barely got out alive and the incident haunted him for some time.

     In 2001, Duke was sent into Russia to track down Major Bludd, who had been on the run for years, and was still wanted for the murder of General Flagg. After a fight and a chase, Bludd escaped, but Duke was led to the room he had been staying in, and found a note left behind by Bludd, telling of a meeting set up by Cobra Commander. It appeared that Cobra had returned to the United States, and Duke's discovery led to the reinstatement of the G.I. Joe team. The team's first new member was Kamakura, who had taken surveillance photos of the Commander's return to the United States under orders from Duke. Hawk once again made Duke the team's field commander, though he apparently no longer holds any formal rank in the military. Often briefing the Joes on their missions, Duke also spends time in the field. Several years after his first mission to the research lab, Duke led a team of Joes to the abandoned lab and fought the same creatures he found years before. This time, his team all made it out and one of the original scientists was rescued, helping Duke to put the original mission behind him. Duke later joined the Joe team in their invasion of Cobra Island to fight the forces of a revived Serpentor.

    Duke came into conflict with members of the team when he hatched a plan to capture Destro in Sierra Gordo. The 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 setting up Destro to be captured. In fact, he hadn't told Hawk or any other Joe what he was planning. Duke personally captured Destro, 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. Before the situation was completely resolved, 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, but soon found himself fighting the cabal of generals known as the Jugglers. 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 did his 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. While Rey and the remaining Joes fought Cobra Commander's plans to unleash the deadly superweapon known as the Tempest, Duke and Scarlett took matters into their own hands to rescue Snake-Eyes with the help of Storm Shadow. 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 also sparked violence and instability around the globe, hoping to take control of the world. 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. In the end, Duke and Rey's small team defeated the schemes of 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 Duke, 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. An obsessive Hawk, still hospitalized, was certain Cobra Commander was behind the incidents and asked Duke to go on a personal mission to find the Commander. Duke reluctantly agreed and cut off all contact with the Joes. He followed clues into South America, where he and a band of mercenaries he hired were attacked by a group of Cobra BATs. Duke was captured and taken to a BAT factory abandoned by Cobra, but still under the control of a deranged Fred-series Crimson Guardsman named Calvin. Duke was beaten and tortured by Calvin but discovered his plans to launch a nuclear missle to kill Cobra Commander. After fighting more BATs and killing Calvin, Duke saw that the missle was targeted at Washington, D.C. Injured, he eventually found his way to a crude medical station run by a doctor named Elizabeth Parker. With all means of communication cut off and no way to warn the Joes, Duke got Parker's help in securing a plane back to Joe headquarters. In Duke absense, it was revealed that Cobra Commander had been disguised as the White House Chief of Staff and created a commando team called the Phoenix Guard to eliminate the Joes. The team's roster included former Cobra operatives led, unwittingly, by General Rey. Believing the Joes had gone rogue, Rey led the Phoenix Guard in an invasion of Joe headquarters. Duke arrived just in time to help the Joes gain the upper hand and defeat the invaders.

    Following the Phoenix Guard incident, Colton ordered the Joes to take time off. While on leave in St. Louis, Duke was approached by General Rey, who asked for Duke's help in investigating his identity, and why he so easily followed orders to stop the G.I. Joe team. Rey knew little of his past, and was ready to fill in the blanks in his memory. Duke grudgingly agreed to help. Their search brought them to Zandar and a fight with the Dreadnoks, and then finally to the former Cobra agent known as Crystal Ball. Rey eventually learned that he was a clone of Serpentor, created to follow the Jugglers' orders without question. Rey found the strength to overcome his programming, and Duke agreed to give him a chance to redeem himself. A short time later, Duke led a team of Joes sent to stop rebel leader Colonel Sharif's attack on a Saudi Arabian oil refinery, and ran afoul of Major Bludd. Duke personally captured Bludd but the team learned that the attack was staged by the Baroness to distract the Joes from her activities during her search for Cobra Commander, who had kidnapped her baby son, Eugen. The Commander soon blackmailed Destro into giving him control of his M.A.R.S. corporation.

    Using the resources of M.A.R.S. and the many government secrets he learned while posing as a White House official, the Commander spread chaos in various nations, literally starting World War III. In the early stages of the conflict, Duke and his father Max were captured by Cobra. The Interrogator tried to force Duke into revealing G.I. Joe secrets by threatening Max's life, but both were rescued by Roadblock. The Joes were then sent to Jerusalem to prevent Cobra's attempted assassination of the Israeli prime minister. The team was informed of the plot by Lorcan Rourke, an old undercover agent who disappeared years before out of shame for incidents in his past. Duke worked closely with Rourke when the Joes were attacked by Cobra's Plague unit in Israel and later in New York City, encouraging the agent to forget his past and move on. Duke and the rest of the core members of G.I. Joe continued to fight the war in various countries, eventually crushing Cobra and arresting Cobra Commander. Today, Duke continues to serve as one of the leaders of G.I. Joe.