While attempting to assist Heero in his gundam's repairs, Duo received a new mission to destroy the Corsica Base. A tough mission considering how his gundam was built for close combat, and it was very far out of the way. Ironically, Heero had also received a new mission for the next day as well and the two of them worked through the night, though they didn't say much to each other aside from Duo expressing his exasperation at Heero's antisocial behavior. He saw Heero off the next morning, amazed at his fellow pilot’s work ethic. Exhausted, Duo passed the work to his shipmates and slept until it was time to leave. That afternoon, he made his entrance at Corsica, taking out the main mobile suit assembly line first, before making his way to the hangers and out to face the considerable amount of Alliance soldiers. Toward the end of battle as he was running low on fuel, an opposing army began firing upon the remaining enemy mobile suits.
With the battle over, Duo faced down yet another gundam and the opposing army’s leader. The other pilot took the first step by stepping out of his suit to greet Duo. Duo returned the gesture, and the two traveled to Quatre's safe house for repairs and a rest stop. The two got along pretty well initially, sharing their respective stories as their mobile suits were repaired. He got to know the 40 Maguanak soldiers quite well during his brief stay as well, but took off the next morning to return to his own allies. Once again, he arrived just in time to go on another mission on an OZ sea base, this time running into Heero again.
Weeks later, Duo is once again called to a mission, this time at New Edwards Base to destroy a meeting of key OZ leaders, which would essentially end the military dominance of Earth Sphere and the colonies and make it unnecessary to fight any longer. He traveled there alongside Heero who he again encountered at an airport, and both were later joined in battle by an unknown suit and Quatre. Just as they pushed back enemy mobiles to a near surrender, their targets were spotted fleeing in an OZ passenger Jet and Heero flew up to cut them down.
In a terrible turn of events, it turned out that the men in that jet were not the OZ leaders attending a conference, but Alliance pacifists discussing the road to peace. The fifth gundam arrived to not only explain that, but to berate Heero and the others for being foolish enough to fall right into OZ’s trap. What’s more, is that the meeting itself was only a lure for the gundams to keep them from realizing that Trieze Khushrenada had staged a Coup d'état against the Alliance. A plot which was being carried out as they stood there in awe.
In the wake of this tragedy, the pilot of the Heavyarms gundam revealed himself as Trowa Barton, son of the mastermind behind Operation Meteor, Dekim. He demanded that all the four gundam pilots serve under him as subordinates so that he would show them mercy for betraying his father after the world had been taken over. The other four gundam pilots openly refused, and Trowa's further insistence prompted Duo to pick a fight with him. The pilot of the fifth suit broke up the scuffle, vowing to settle the score with Trowa at a later time himself. He meanwhile had plans to assassinate the man behind the curtain, Trieze Khushrenada. He left the battlefield, leaving the other four to take care of the remaining troops on their own. Outmatched and out of bullets, Trowa withdrew himself to take off back to his own base, making it clear in a thinly veiled threat that their mutiny would cost them.
Unknown to the pilots left at New Edwards, the remaining OZ soldiers on base had activated a missile cluster that lay just under their feet. Quatre sent Duo to retrieve three aircraft carriers, while a former Alliance major Sally Po prompted Heero into action. Duo and Quatre were forced to put their faith in the other pilot’s hands, and they were wise to do so as Heero had been successful. Duo retreated back to the Sweepers once again, disgusted both by what Trowa had said and the actions that OZ had taken to destroy them.
Two weeks later, Duo received a message that shook him to the core. The Barton Foundation had seized mobile suits throughout the alliance space force and the colony in the L5 cluster. There was absolutely no question that Dekim was planning on dropping the colony. Sending a relay message to the other three pilots, he rushed to a space port to steal a mobile suit carrier shuttle to make it into space. If by his prompting or their own independent sources, the other pilots and Trowa were all heading for space though it was clear that Trowa would beat them there. Once in orbit the four converged into Lagrange Point 5, only to be blocked by Trowa and his small army of mobile suit troops. For gundams who were not calibrated for battle in Zero G, Trowa’s managed to keep them bay quite effectively Heero managed to break away to try and blow away the colony before it hit, but he only managed destroy a small fraction of the colony, only to watch the rest plummet to Earth. The colony landed in Europe, decimating the continent and OZ’s headquarters in one fell swoop. Those who didn’t die instantly would die from radiation or worse. Survivor would be forced to head to space until the Earth could be restored. Seeing the depths of their failure, the gundam pilots fled to their respective colonies.
Duo reunited with his gundam's engineer in the L2 colony and they took refuge in an unused resource satellite so that Professor G could modify his gundam for universal maneuverability capabilities. Combat in both space and on Earth would be necessary, but all they could do now was bide their time and hope that Dekim would focus his efforts on the Alliance space force and OZ on Earth. Through his activities waiting for the old man to fix his Deathscythe, he met with Alliance soldiers and civilians and assisted them in any way he could without giving up his cover. He made many allies, even among those he would have once considered his enemies. His main source of comrades came from former OZ and Alliance among his other sweeper allies. Though he didn’t know if their helping him came via orders from the top. It didn’t matter, so long as they didn’t betray him.
Meanwhile, Dekim began his public campaign, using his resources to fund relief efforts and at the same time, demonizing OZ and certain organization such as the Sweeper Group and the Colony Liberation organization. The people were divided, but Dekim quickly earned support from several key leaders through coercion, money, or threats. In that time, Duo noted that both Heero and Quatre had fallen completely off the radar, and it wasn't til months later that he discovered that they had both been captured by Barton. It was only a matter of time before they caught up with him as well, so long as he stayed with the sweepers and he wasn't about to abandon them.
At the end of AC196, Dekim had seized complete control of both the Earth Sphere and all five colony clusters thanks to Earth's weakened state and the Alliance's failure to compensate for it since Trieze's Coup back in New Edwards. The only thing Duo could do at that point was fight back, and with his upgraded gundam, he did just that. With Deathscythe on the war path, he was soon periodically joined by Wufei and his newly modified Altron Gundam, fighting Barton's mobile suits, often with Trieze's soldiers backing him up. With new weapons on Dekim’s side called Mobile dolls, fighting back was no easy feat, but they found a way. Between the OZ and the Aliance, their numbers were still horribly pitiful.
After one such battle, the two gundam pilots returned to a safe location run by Sweepers in order to have their gundams repaired for the next conflict. It was then that the two pilots were able to find common ground. Duo, who imparted his mechanical knowledge to Wufei, and Wufei assisted Duo by helping him refine his hand to hand combat techniques. The two still found it somewhat difficult to get along, but they had begun a very interesting friendship. They went on several more missions over the course of two months and split company during their last battle for resupply and repairs.
A few days after parting with Wufei, Duo was tracked down to his hanger on the L2 colony and ambushed by Trowa and his soldiers. They restrained him and loaded his gundam to a transport unit, driving it off. Trowa stayed behind to inform Duo that not only had he been expendable from the very start, but he'd been ordered killed by his father. The man beat the pilot savagely, leaving Duo bruised, bloody and barely coherent. In one last act of cruelty, Trowa yanked Duo's head back and severed his braid near the base of his scalp with a knife. Being in the state that he was, Duo was only vaguely aware of what had happened and it soon went by the wayside. He no longer had the energy to retaliate or react in any manner by which Trowa was entertained by. Bored with his captive, Trowa decided to cool down and end it.
While Duo was sure he was at Death's door whether or not Trowa made the finishing blow, it all seemed to stop. His ears rang, clouding the noises of two men talking, Trowa sounding upset. One of Trowa's assistants had come in to report on the progress of getting the gundam off the colony, and there had been a snag that Trowa had to see to immediately. He ordered the guy he called No-Name to watch over the gundam pilot as he left to get the problem solved so he could get back to his work, though he also said it was to savor the kill. That Duo heard quite clearly. After about five minutes for what seemed to be forever, the assistant went to Duo and untied him. The two of them were joined by several other soldiers who took Duo and placed him on a stretcher, bringing him out to an ambulance.
He was soon revived into a hazy reality where he was overseen by No-Name, Lieutenant Lucrezia Noin and Colonel Une. He was transported to the Moon Base to settle in to his recovery. It wasn't until the next few days that he realized the full extent of the damage done to him, discovering the loss of his braid left him lethargic and mildly depressed. Wufei returned to check up on him, but at first it seemed like he was just adding insult to injury. Eventually, Duo let down his defenses and allowed himself to laugh at his friend’s persistent jabs at his ego and appearance and let it slide. Injured as he was, he was effectively sidelined until further notice. After about a month in recovery, he spent a lot of time getting to know No-Name and several other soldiers on base. It turned out that the OZ soldiers had nicknamed him Tonio, after the character from a opera about a clown. Given Tonio’s previous profession it fit, but he expressed that he didn’t much care for it.
Planning stages were brought to the table for use of new mobile suits against the Barton Foundation. Une, who had gathered together the five gundam engineers, had them design and build a new type of mobile suit, potentially superior to the gundams. They were called Mercurious and Vayeate. The two suits were designated to Zechs Merquise and 'Tonio', with Wufei going in as their back up in a plan to invade Barton's colony X18999. By missions start, Duo was still grounded, staying behind to hold down the fort. However, that didn't mean that he wasn't himself tasked with a job to do.
Even though Duo wasn’t up to form, Professor G and Doctor J sent him across the moon in an effort to collect the battleship Peacemillion alongside Lieutenant Noin. A few days into the search, Duo got word of a mission success, at a cost of heavy damage to Deathscythe which had been locked in heavy battle with Altron. However, they did manage to retrieve Heero, Relena and Quatre as well as their gundams in this successful assault. This prompted an attack on the moon base which stretched their limited resources and forced them to make a retreat on the battleship.
Falling back to resource satellite MOII, the gundam pilots met with Howard and the sweeper Group, who took command of the Peacemillion which freed the hands of the soldiers and pilots for other tasks. Duo spent most of his time on the sidelines for the next few battles until his gundam was complete, thinking that he’d be battle ready at about the same time as his Gundam. Sometime later, they were also joined by an impressive number of OZ soldiers and Trieze himself. For the next few months there were several key battles for various locations in space, with victories on both sides. While Dekim’s oppressive rule was beginning to be questioned among the people and Princess Relena’s support granting the Gundam’s the image of a force for peace in the world, Dekim’s world was beginning to crumble. The gundams launched one final attack on the Barton’s mobile doll plant in an effort to remove his main force. Their only obstacle being Trowa and hundreds of mobile dolls. Duo and Wufei took on Trowa due to Heavyarm’s lack of short range battle options and their speed of movement, while the others went straight in to destroy the base.
At the end of the day, Trowa was defeated and arrested, and the main source of Barton armaments destroyed. Better yet, it was reported that Heero had killed Dekim and retrieved Mariemeia. Once they brought her back, Heero passed the girl off to Duo to deal with. He managed to establish a rapport with the girl as they waited for her father to come for her, which took almost three days. He bid farewell to the young girl and took his leave.
With the war over, Duo went back to L4 with Quatre to draw up plans for a habitat restoration program that his father Zayeed has begun working towards. He has all the intention of going to Earth with a work crew, but Quatre told him his place was in the colonies to work behind the scenes. That was where they were needed. So that’s where he’s been, trying to enjoy the unstable peace as he could and buried himself in his work.