In 2001, several years after the defeat of Cobra and the disappearance of Cobra Commander, reports of Cobra activities in the Middle East, Europe and South America led by the Commander began to come from the world's intelligence agencies. He had been rebuilding Cobra by recruiting disaffected soldiers from around the world. When spy photos taken in the Florida Everglades proved that Cobra Commander was in the United States. He contacted many of his former high command and called them to a meeting at the Florida headquarters of the Dreadnoks -- now an organized, national biker gang. He revealed his "nano-mites" -- microscopic machines that can be used to infect the world's computer systems and the human body. Before his plans could come together, Destro arrived and forcibly took over Cobra. He infected the Commander with nano-mites, leaving him ranting, raving and barely coherent. As Cobra Commander sat in a padded cell, Cobra troops and Iron Grenadiers, all under Destro's command fought a reinstated G.I. Joe team's effotrs to stop the nano-mites from bringing the country to a standstill. As the forces faced off in Washington, DC, the nano-mites were deactivated and Cobra Commander was rescued from his cell by Storm Shadow, still obviously effected by the Brain-wave Scanner.

    With Tomax, Xamot and his old ninja bodyguard by his side, the Commander tricked all the members of his former high command (except Destro) back together and revealed himself. Threatening them with Storm Shadow's wrath, he told them they would continue to serve him and he decided to spare their lives in exchange for them continuing to work for him to pay the debt they owed him. He then attacked Destro's castle in Trans-Carpathia, planning to kill Destro for his betrayal. Destro revealed that the man who had taken Cobra from him was actually Destro's son, Alexander, working on his own. To make up for what happened, Destro offered his services to Cobra as long as the Commander saw fit. He agreed, and was ready to continue the business of Cobra with all of his old lieutenants working for him.

    The Commander once again went up against the Joes, sneaking a nuclear device into the country even as he sent Storm Shadow to assassinate General Hawk, and set many more plans into motion. When Storm Shadow nearly broke free of the brainwashing at the Commander's hands, the Commander reached the ninja before Snake-Eyes and Billy could help him and gave him a refresher session with the Brain-wave Scanner. The Commander escaped Snake-Eyes after shooting his son, Billy and got away with Storm Shadow's help once again. On his way back to safety, the Commander was attacked and kidnapped by unknown agents. He was brought to Cobra Island where he was shocked to discover Serpentor had been revived by former Cobra troops and was being assisted by Dr. Mindbender. His old rival had built his own army of followers known as the Coil and had attacked several major cities around the world. The Commander escaped his cell with help from some captured Joes, and sent out a radio message to Destro that all debts would be paid if he rescued the Commander. As he made his escape, a G.I. Joe invasion force arrived, soon followed by Destro's troops, Cobra, and the Dreadnoks. As the battle raged, the Commander was confronted by Serpentor on a Firebat launchpad high over a waterfall, as Mindbender looked on. The Commander fought the former Cobra Emperor, but was no match for him. Serpentor told him to take off his helmet before he killed him. The Commander handed over the helmet, only to have it explode in Serpentor's hands. Cobra Commander taunted the bloodied and dazed Serpentor, "You were engineered with such potential, Serpentor. But you lack the most important DNA of all... Mine," then kicked him off the launchpad into the water below. Mindbender ran off as the Commander shouted that he would never escape him. "You'll never run far enough!"

    In the wake of the battle on Cobra Island, Cobra Commander disappeared, and went into hiding with Storm Shadow in a secret Red Ninja retreat in Tibet, where he hoped to recruit the ninjas for Cobra. He barely escaped when the Joes found the ninja hideout. He finally returned to retake his organization from Destro, who was eager to turn over command and return to Scotland, his debt to the Commander finally paid. Thanks to Tomax and Xamot's efforts, Cobra regained control of Cobra Island, and Cobra Commander was ready to once again terrorize G.I. Joe and the world. But the Joe team's capture of Destro in Sierra Gordo put a damper on his plans. The arms dealer was about to go on trial in front of the United Nations when he made a deal. He would not reveal any of the dirty secrets of certain country's government arms deals if he was let free, and he offered to help them finally capture Cobra Commander. The Commander was baited into action by being told Destro was on a train being guarded by the Joe team. He also thought that the Baroness had turned her back on Destro. In reality, Destro had all ready been released before the Commander led an attack on the train. In the midst of battle, Cobra Commander fought Hawk hand-to-hand and when he had a brief advantage he shot the Joe commander in the back at pointblank range. But moments later, the Baroness shot the Commander, who was quickly taken into custody by the Joes even as a paralyzed Hawk was rushed to a hospital.

    The Commander was then taken to a federal installation to await interrogation -- or so it seemed. In reality, it was not the Commander who had been arrested at all. It was Zartan in disguise. Some time earlier, Zartan and the Commander has switched places. Sensing treachery, the Commander took Zartan's place at his Dreadnok compound while Zartan attacked the train supposedly holding Destro. Cobra Commander eventually rescued Zartan and made his way back to Cobra Island, where Destro was now running the organization. Destro had no idea that Major Bludd, Tomax, Xamot and others had remained loyal to the Commander all along, and allowed him to get past the island's defenses. Destro sent away the pregnant Baroness and his bodyguard Wraith to escape in a plane, the Commander fired a missile that destroyed the aircraft, presumably killing the Baroness. He then took control of the weapon known as the Tempest, a device that could seed the clouds to make it rain. With Dr. Mindbender's help, it was used to make the flash-eating Death Angel virus rain down upon a chosen area. The test of the weapon prompted the United States to deal with Cobra's threat once and for all and drop a nuclear bomb on Cobra Island. Cobra Commander was made aware of the bombing plan by the corrupt General Gibbs, and devised a way to use the bomb to carry out revenge against his enemies. The Commander, his loyal Cobra soldiers, and a number of prisoners including Destro took off from the island. Those that remained on the island had all been members of the Coil who rejoined Cobra under Destro's leadership. Taunting them with one final video message as his aircraft left the island, Cobra Commander informed the Coil troops that they were going to pay for their treachery. Seconds later, a G.I. Joe pilot dropped a nuclear bomb, effectively destroying Cobra Island. The Commander set up a new Cobra headquarters in the European nation of Badhikstan, and prepared to launch the Tempest into orbit onboard a satellite. After Dr. Mindbender finished preparing the Tempest, the Commander shot him, finally putting a stop to his years of betrayal. Soon, the G.I. Joe team lead an assault on the Cobra base. The Joes defeated the Cobra troops there, and destroyed the Tempest with help from Dr. Mindbender -- his final act before bleeding to death from the Commander's gunshot. Cobra Commander himself escaped with Tomax and Xamot to hide out in a cave somewhere in Badhikstan. It was there that he was confronted by a gun-wielding Dela Eden, a member of the Red Shadows -- a secretive group that sought to do away with G.I. Joe and Cobra in order to reach their goal of world domination.

    Cobra Commander's fate was unknown following his confrontation with the Red Shadows. Hawk, hospitalized and obsessed with finding the Commander, sent Spirit on a secret mission to track him down. Spirit spent months following clues and rumors to South America, where he heard locals speaking about "The Blue Ghost," who was associated with the disappearance of local criminals, whom Spirit presumed were recruited by the Commander. Spirit eventually reached a cabin in Southern Peru and was surprised to the find the Commander there, expecting Spirit's arrival, and holding the Joe at gunpoint. Spirit was captured and thrown into a cell, where he stayed for some time as the Commander set his latest plan in motion.

    Though the G.I. Joe team did not learn this for nearly a year, Cobra Commander slowly began to rebuild Cobra has he had once before. By means still unknown, he killed White House Chief of Staff Garrett Freedlowe and took the official's place with the help of technology borrowed from Zartan. Now posing as one of the President's closest advisors, the Commander gained unprecedented access to government secrets. He attempted to convince the President that the newly reactivated Joe team was not only unnecessary, but not to be trusted. The President trusted "Freedlowe's" advice and allowed him to create a special missions team called the Phoenix Guard to replace the Joe team. The team's leader was General Philip Rey, who had no idea of Freedlowe's true identity. And unbeknownst to Rey, the soldiers assigned to the team were all former Cobra agents under assumed identities. Rey was told the Joe team had gone rogue, and the Phoenix Guard was soon sent to invade and take control of Joes' new headquarters. Though Rey ordered there be minimal loss of life, the disguised Cobras caused extensive damage to the base, injured a number of Joes and killed even more of their support staff. As his team secured the base, Rey discovered who they really were and helped the Joes defeat the invaders. Joe commander General Colton contacted the President who knew nothing of the attack. He realized Freedlowe was behind it, but he and the Secret Service discovered his long-dead body in Freedlowe's office. Cobra Commander's face appeared on a nearby video screen, informing the President of his deception. He added that he now knew the country's greatest secrets and weaknesses. Back in his base of operations, the Commander planned to activate a number of hidden Cobra cells and launch his new plan for victory. And unknown to all but his closest lieutenants, the Commander now has the Baroness' newborn baby under the care of Cobra doctors. His plans for the future remain unknown.