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. The mission involved the Hammer Team, which was made up of a small group of soldiers, including Sean Collins, son of Wade Collins. Only a week before his planned marriage 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. Also scarred by the incident, Sean Collins took some time off from the Army and tracked Snake-Eyes down at his mountain cabin, hoping the commando could help him deal with the pain and anger over what he had seen. Snake-Eyes agreed to train Sean as a ninja, eventually with the help of the remaining members of the Arashikage clan -- Jinx, Nunchuk and T'jbang. Sean came to call Snake-Eyes "Silent Master." Almost another year passed, and Jinx discovered that Firefly was in Tokyo to meet with the "Nowhere Man", an unidentified man who was recruiting soldiers and mercenaries, including former members of Cobra. While tracking Firefly, Sean, Snake-Eyes, Jinx and Budo had the mercenary under surveillance when he met with Storm Shadow to recruit him. A confrontation followed and Snake-Eyes once again fought his sword brother, even as the others tried to capture Firefly. Duke and Chuckles arrived on the scene and soon intervened to help the ninjas evade the Nowhere Man's men. Duke revealed that the Nowhere Man was actually Mikhail Derenko, a soldier who had pretended he died with the rest of the Hammer Team. Sean was now determined to get his revenge on Firefly for killing his friends and Derenko for betraying him. At a nightclub in Japan, the mercenaries and the former Joes fought again as Derenko and his men attempted to access an old Cobra weapon. The plot was foiled, though Derenko escaped and Sean's father, Wade was killed while helping the Joes. Weeks later, having passed his final trials, Sean was officially welcomed into the Arashikage clan at Snake-Eyes' cabin, naming himself "Kamakura" after the clan's golden age.

    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 (including Kamakura) and Snake-Eyes was one of the team's highest ranking field commanders. Scarlett was 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 are again engaged to be married, but continue to work with the Joe team. Snake-Eyes once again came face to face with Storm Shadow, who was again working for Cobra, and was sent on a mission to assassinate Hawk. The two former friends fought, and Storm Shadow claimed that he still held a grudge against Snake-Eyes for his supposed favored status given by the Hard Master years ago. As he made his final escape, the ninja slashed his sword at Snake-Eyes face, tearing another scar across it. For a moment, Snake-Eyes let his anger get the best of him as he fired wildly into the ceiling into which Storm Shadow escaped.

    After that encounter, Snake-Eyes' many missions for the new team included battling mutated soldiers in the arctic and rescuing Flint and the Baroness from Russian mobsters. He and Scarlett then returned to their cabin for some time off, but were interrupted by Billy (now going by "William"), who had received word from Storm Shadow that he needed Snake-Eyes help to make the final break from Cobra Commander's mind control. By the time Snake-Eyes, Kamakura and Billy reached their fellow ninja, he was again subjected to the Brain-wave Scanner by Cobra Commander himself. A fight followed, but in the end, Storm Shadow chose to return to the Commander's side. Snake-Eyes had also helped track down a group of mysterious children who turned out to be clones of the original Serpentor. As a convoy of Joes escorted the children to a safe location, forces led by a revived Serpentor attacked, taking the children with him and capturing Snake-Eyes and several other Joes. As the Joes escaped their jail cell on Cobra Island, Snake-Eyes was seriously injured and had to be carried the rest of the way. Soon, on one of their biggest operations ever, the Joes led an assault on Cobra Island that led to victory.

    Snake-Eyes recovered from his injuries and returned to duty soon after for a mission into Tibet after a transmission was sent out by T'jbang, who had infiltrated the lair of the current group of Red Ninjas, hidden in a mountain cave in Tibet. T'jbang's mission was not authorized by Hawk, even though Snake-Eyes had given T'jbang access to G.I. Joe equipment. Hawk was angry at Snake-Eyes for keeping him in the dark, but knew he was the best choice to investigate, though he placed Scarlett in command of the mission. Hawk added that if Snake-Eyes had the chance to stop Storm Shadow, he had better put his feelings aside and deal with him. Snake-Eyes and the others discovered Cobra Commander and Storm Shadow had formed an alliance with the Red Ninjas' new leader, Sei Tin, who intended to make the group into more than just a remnant of the Arashikage clan. The Joes' team arrived in Tibet, along with Jinx and Kamakura. After a battle with the Red Ninjas, Snake-Eyes fought Sei Tin and won, as Storm Shadow and Cobra Commander escaped the cave. The Red Ninjas were happy to accept Snake-Eyes as the new leader of the clan, and he passed that leadership on to T'jbang. After their return home, Hawk's anger continued, now also angry at Scarlett since they both let Storm Shadow slip away again. The two Joes remained on probation during their mission into Badhikstan, where they fought Cobra forces, including the cyborg Overkill, who was in reality the SAW Viper Snake-Eyes had left for dead years before in Benzheen. He bested Overkill, and though the deformed, half-robotic said that he welcomed an end to his life, Snake-Eyes refused to kill him.

    While the mission in Badhikstan was coming to an end, Hawk had been shot in the back during a battle with Cobra Commander and left partially paralyzed. With Hawk confined to a hospital, the Joe team tried to continue on, with command shared by Duke, Flint and General Joe Colton. With the Joe team's future uncertain, The Jugglers once again began cracking down on the team. When a mission into the Cobra-infiltrated town of New Moon, Colorado that included Snake-Eyes and other Joes ended disastrously, 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.

    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, Snake-Eyes helped rescue him as he and Scarlett 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. 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 Snake-Eyes, Scarlett 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. Snake-Eyes tracked down Firefly in Chicago, interrupting the mercenary's assassination of a gang leader. After a brief fight between them, a group of gang members appeared and attacked both Snake-Eyes and Firefly. Firefly used explosives to stop them and make his escape.

    Snake-Eyes returned to the Joes and learned that though the attacks had been stopped, Scarlett had disappeared during her investigation. Using Scarlett's microscopic tracking device -- she and Snake-Eyes had them implanted to keep track of one another in an emergency -- they found she was in the middle of the Pacific Ocean. In reality, she had been captured by Destro and was being held on his submarine. The Joes then went on an unauthorized rescue mission as Colton looked the other way. During the mission a fight between the Joes and the Iron Grenadiers ensued. 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 the Joes 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, now dressed all in red, had been brainwashed by the ninjas to be used as a weapon. Some of the Joes were captured by the ninjas pleaded with Snake-Eyes to get their old friend back. 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 felt changed by his experiences and decided to turn his back on his life as a ninja for a time. While Snake-Eyes was stationed at the Joes' new headquarters, The Rock, Storm Shadow revealed to him and Scarlett that the Baroness was being held prisoner there, 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 quite, 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 Snake-Eyes, 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. Spirit and Snake-Eyes saved Rey from being killed by Scrap-Iron, and 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 Snake-Eyes 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.


Artwork: G.I. JOE vol. 2 #1 (cover) by J. Scott Campbell; G.I. JOE: America's Elite #12 (cover) by Phil Noto.