The boy named Billy was born to a loving mother and a father losing his grip on reality. His father's growing insanity would become a curse that would affect Billy's entire life. Some time before Billy was born, his father's beloved brother, Dan, died in a car accident. Billy's father was devastated, and barely acknowledged that his brother had been drunk at the time, as well as since his return home from Vietnam had, had a death wish, and the fact that he killed a family of three in the accident as well. His brother's death helped push him over the edge. His failed business and dwindling finances also took it's toll on him. He hired a man to kill the surviving son of the family in the other car, and nearly bankrupted the family to do so. After Billy's birth, his mother learned what her husband had done, and was outraged as well as horrified. Soon, Billy's father left, taking Billy with him. Traveling the country, he began his plan to stop the government and big business from destroying "the little guy". It began as a pyramid scheme to sell products to gain power and money, but over time it became more. Billy's father began to attract followers who, like him, had faced failures in their lives, and were ready to listen to a man willing to circumvent government and to blame failures on everyone but himself. As he traveled the country, having meetings in seedy motels in small towns full of disenfranchised "little guys". He soon named his organization "Cobra" and Billy's father was now known only as "Cobra Commander". All the while, he dragged Billy along with him. At first, the child didn't understand what his father was doing. He was even told that his mother died years before. But as Billy grew older and his father gained power in a nice little town called Springfield, the boy started to realize who and what his father was. Eventually, Billy couldn't stand what his father was doing and ran away. He never made it out of Springfield and fell in with a small resistance group of townspeople who didn't want anything to do with Cobra. Over time, Billy blocked out the painful memories of who his father really was.
After Cobra had become an international terrorist threat, the G.I. Joe team stumbled upon Springfield. Scarlett, Zap and Snake-Eyes were captured. The Joes found themselves drugged, and in a jail cell with young Billy. He never told them his name, but he helped the Joes escape. He stayed behind in the town hoping to continue fighting against Cobra's control. Years later, Cobra agents Major Bludd and the Baroness sought out a young member of the resistance group to turn into an assassin. They hoped to kill Cobra Commander and usurp his power. Neither they nor Billy knew that he was the Commander's son. The two Cobras ruthlessly trained Billy, molding him into the assassin they needed. Billy was soon set to strike at a Cobra rally, as one of the Young Cobras (a group that warped local children's minds to serve Cobra when they grew older). Billy was carrying a bouquet of flowers for the Commander, but among the flowers was a pistol. The boy stepped up to the Commander and pulls put the weapon. But Destro recognized who the boy was, and couldn't watch him kill his own father. He lunged at Billy and knocked the gun away, saving Cobra Commander. Face to face with the Commander, Billy heard his voice and recognized his father. Cold and heartless as ever, Cobra Commander ordered an inquest to learn who put Billy up to the assassination. Billy was strong willed, however, and refused to identify his accomplices. The Baroness and Major Bludd were pleased of course, but the ninja Storm Shadow was disgusted that those responsible would let the boy be punished on his own. Storm Shadow also admired the boy's integrity. Billy was thrown in a cell beneath Springfield, and was surprised when Storm Shadow arrived. He made quick work of the guards and helped the boy escape. Billy convinced Storm Shadow that the ninja couldn't stay either. He agreed and they both headed to New York, and Storm Shadow's personal training dojo in the city. Cobra Commander, meanwhile, quickly gave up on his son, and returned to Cobra's business.
Over the next few months, Storm Shadow trained Billy in ninjitsu. He not only taught Billy to fight, he also taught him the honorable ways of the ninja. He came to see Storm Shadow as a surrogate father. Even so, Billy decided he had to confront his father. He left his teacher a note, and started on his way, hitch-hiking back to Springfield. Eventually, Billy was picked up by a driver who had earlier picked up Rip-Cord's girlfriend, Candy. Soon, they both realized the driver was drunk, and Billy saw a vision of death. At a railroad track, the driver lost control of the car. The car crashed before hitting the train, catching on fire. Escaping Springfield as they approached, was the Soft Master. He was being chased by Cobra agents Firefly, Scrap-Iron and the Dreadnok Buzzer. He turned back to help those trapped in the car, but the Cobras caught up to him. As he tried to help the passengers (who were unconscious) out of the car, Scrap-Iron fired a missile at him. The old ninja master stopped the first rocket himself, but Scrap-Iron fired another. The car was hit and exploded, and those inside were presumed dead. The car's driver and Candy were both killed, but Billy survived, barely. He spent months in a coma, and lost a leg and an eye.
Billy eventually came out of his coma, and was surprised to find his father by his side. Cobra Commander had discovered Billy's survival and found his son in a hospital outside of Springfield. Vowing to be the father he had never been, he took Billy to the undercover Crimson Guardsman; Fred VII. Fred was a mechanical genius, and the Commander asked him to build a prosthetic leg for his son. Fred did so, and Billy could walk once again. At first, Billy didn't remember his imprisonment in Springfield and his training under Storm Shadow, but he stumbled upon the martial arts school of the Blind Master (a member of the same clan as Storm Shadow). This sparked Billy's memory and he recalled all that had happened. He confronted his father and then stormed away, not wanting anything more to do with him.
Billy began training once more, this time under the Blind Master and his student, Jinx. Billy also learned that Jinx had ties to the G.I. Joe team. He vowed that he would not betray his father to them, but Jinx told him they would not ask him to do so. Later, Jinx took Billy to the Presidio Army Base in San Francisco. He thought he was being forced to take lessons in speaking French, but he found his way to a secret basement of the Language Center building, where Hawk and other Joes waited for him. Hawk brought Billy to meet with Rip-Cord and Storm Shadow. He told them what had happened to Candy and the Soft Master. Just then, Hawk received word that Scarlett and Snake-Eyes (who had been on vacation in Grenada with Flint and Lady Jaye) were killed after stepping on a land mine. Storm Shadow was skeptical. He didn't believe a ninja would be so careless as to stumble upon a land mine. He eventually learned that they had faked their own death so they could embark on a secret mission to rescue Stalker, Quick Kick and Snow-Job from a Borovian gulag. The Blind Master had helped them deceive the others. Storm Shadow decided he had to help his friends, and journeyed to Borovia, with Billy and Jinx in tow. They all succeeded in rescuing the captured Joes, and returned home to San Francisco. For a time, Billy continued to train with Storm Shadow, who helped Billy and Jinx run the Arashikage Martial Arts Academy in downtown San Francisco.
Months later, the three ninjas were called upon again by the Joe team. In the aftermath of the Cobra Island civil war, unscrupulous officials arrested much of the G.I. Joe team, and locked up Hawk and General Hollingsworth in a mental hospital in Virginia. The remaining members of the team went underground, and staged a rescue. Billy, Storm Shadow and Jinx joined them, and soon the Generals were freed and the team was cleared of any wrongdoing. Some time after that incident, Jinx was met at the Presidio Army Base by an armed woman, claiming to be Billy's mother. She brought her to the Martial Arts Academy and she and Billy acknowledged that it was, indeed his mother. She had tracked him down after years of searching. She relayed to the ninjas the story of how her husband came to leave with Billy. She asked Billy to come home with her, hoping to start over. Billy agreed, and for a time he lived with his mother. Soon he began attending college, and began enjoying a normal life. That wouldn't last for long.
On the way to class one morning, Billy was stopped by the Cobra agent; Raptor. Raptor told Billy that his father had been killed a few years ago by Fred VII. Fred had in fact been posing as Cobra Commander for some time. They made their way to Cobra Island where they confronted Fred along with other Cobra operatives in the Island's land-locked freighter. It was then, that the true Cobra Commander returned. He hadn't died years ago, but had been in hiding, biding his time until he returned. He threw others into the freighter with the rest of the "traitors". Calling his past decision to go straight "irrational," he disowned Billy as his son. He planned to seal the freighter and kill all those inside. Billy shouted to his father, "You kill more than just a ship full of people if you kill us! You kill your own humanity!" The commander just laughed. "That was killed long ago," he said, "when my own son tried to kill me!" Using explosives, he then buried the freighter under the rubble of the island's volcano. Some time later, Cobra troops found the buried freighter and they discovered that though there were many bodies inside, two could not be accounted for: Billy and Zartan. It appeared that Billy had once again cheated death. He and Zartan made their way to Scotland where they hoped to get Destro's help. They managed to arrive just as Cobra Commander was staging an attack on Castle Destro. The Joes were there as well, expecting trouble and trying to help Destro. Billy and Zartan managed to rescue Destro and Chuckles during the attack. After a chase through various countries, they joined forces with the Joes, along with Storm Shadow and the new G.I. Joe Ninja Force team. Together they stopped Cobra Commander's plans.
Billy spent the next few years traveling around the world, happy to avoid conflict and have some peace for once in his life. He eventually found his way to Destro's new castle in the mountains of Trans-Carpathia, and spent some time there as friends with Destro, Zartan and the Baroness. Around the same time, Cobra Commander was taking control of the nation of Borovia. Though he now backed a legitimate government, he became worried that Destro, in nearby Trans-Carpathia, was a threat to him. Using Dr. Mindbender's expertise and the Brain-Wave Scanner, the Commander managed to brainwash Destro, the Baroness, Zartan, Storm Shadow and Billy. He now had the original "high command" of Cobra back in power, against their will. A short time later, the G.I. Joe team was disbanded by the U.S. military. Soon afterward, Cobra forces fell to a unified attack by regular military forces. Most of Cobra's "high command" disappeared in the wake of the conflict, as did Billy. In the years following, Billy broke free of his father's influence, though he remained emotionally scarred from his brainwashing.
In 2001, Billy was using the name William Kessler and living in Scotland when the reinstated G.I. Joe team enlisted his aid to help rescue Snake-Eyes and Scarlett, who had been captured by a revived Cobra. A short time later, William requested membership from the Joes, vowing to help stop his father. Some time later, William received word from Storm Shadow that he needed Snake-Eyes' help to make the final break from Cobra Commander's mind control, and he headed to the commando's cabin to ask for his help. By the time Snake-Eyes, Kamakura and Billy reached their fellow ninja, he had again been 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.
Months later, Storm Shadow had finally broken free of the Commander's mind control and headed to Japan to distance himself from his past and embrace the Arashikage traditions once again. Billy reunited with his old mentor, who now trained a young woman, Junko Akita, as his new apprentice. She and Storm Shadow also became lovers. When Junko was kidnapped by the Red Ninjas, Billy and Jinx helped Storm Shadow discover that Junko had been taken to the Red Ninja's retreat in Tibet. Along with Budo, Snake-Eyes and Kamakura, the ninjas made their way to Tibet and found that Junko had been brainwashed by the evil ninja Sei Tin. After a brutal battle with the Red Ninjas, Billy and the others could not stop the disturbed Junko from leaping to her death in a ravine inside the cave retreat. The surviving Red Ninjas pledged their loyalty to Snake-Eyes once again, as they had months earlier when he was declared their new leader. Days later, a ceremony was held in the mountains honoring those who had died in the battle. It was there that Snake-Eyes turned leadership of the Red Ninjas over to Billy. The last remaining ninjas resolved to become the foundation of the new Arashikage clan, and Billy pledged to carry on their traditions.