Storm Shadow was born in San Francisco to a family of Japanese immigrants. As a child, he was known as Tommy, and he grew up in an American lifestyle while still learning about his own culture. Still a teenager, Tommy traveled to his family home in Japan. He learned that his family was also a respected clan of ninjas. Tommy studied with his uncles, the Soft Master and the Hard Master. He also spent time with his younger cousin, known as Jinx. Tommy became quite skilled and was granted the title of the Young Master. When he was old enough, Tommy enlisted in the army to fight in Vietnam. His family saw a real war as a "graduate school for their prized pupil." Serving on Long Range Recon Patrol (LRRP), Tommy honed his skills, learning the art of stealth better than he could at home. During his time in Vietnam, Tommy met Snake-Eyes. On their first tour of duty together, they became friends, as close as brothers. Tommy even offered Snake-Eyes a place in the "family business" when they returned home. Their first tour came to an abrupt end when a battle resulted in the deaths of the rest of the soldiers in their unit. They were eventually assigned to a LRRP unit under the command of Lonzo "Stalker" Wilkinson, accompanied by three other soldiers: Wade Collins, Ramon Escobedo and monkey Saperstein. The group stumbled upon an encampment of North Vietnamese soldiers and a firefight ensued. Collins, Saperstein and Escobedo were all believed killed in the attack. Snake-Eyes, Stalker and Tommy all retreated to a landing zone for rescue. As the three soldiers ran across a field toward the extraction chopper, they were fired upon. Snake-Eyes was hit badly and Stalker ordered Tommy to leave him. Tommy refused, running back to save his friend and to Stalker's amazement, he evaded all enemy fire and retrieved Snake-Eyes and the photo of his sister that was so important to him. Recovering from his injuries, Snake-Eyes was sent home only to find his family had died in a car wreck, on their way to meet him.
After the deaths of his family, Snake-Eyes accepted Tommy's offer to join his ninja clan and study in Japan. As months wore on, Snake-Eyes became as skilled as Tommy and in some ways surpassed his skills. Tommy, known in the clan as "The Young Master", was still the most skilled at the bow, but he often hunted animals to prove his skills. A rift started between the two friends since Snake-Eyes did not approve of Tommy's unnecessary killing. What made matters worse was that Snake-Eyes was starting to replace Tommy as the Hard Master's favorite student. Soon, Tommy's world was shattered when the man who would be Cobra Commander hired two assassins, Zartan and Firefly, to kill Snake-Eyes. Hard Master was instead the one killed, and the assassin had used Tommy's arrow to commit the murder. After the murder, Tommy saw the true killer escape, and he knew that he would be blamed for killing his uncle. He fled Japan and sought out his uncle's assassin to exact his vengeance. He eventually joined Cobra under the name "Storm Shadow," a rough translation of his family name, "Arashikage."
Several years after leaving Japan, Storm Shadow was guarding Destro's castle in Trans-Carpathia where Scarlett was being held prisoner. He fought a mysterious commando, who defeated him and escaped with Scarlett. Storm Shadow was not certain, but he thought the mysterious commando may have been Snake-Eyes. Storm Shadow was acting as Cobra Commander's personal bodyguard when he was captured by the Joe team. Though he escaped, Gung-Ho had seen the clan tattoo on Storm Shadow's arm and noticed Snake-Eyes wore the same tattoo. This sent Snake-Eyes to track down the Soft Master, who had been investigating the murder his brother (the Hard Master) for years. Soon, the two former friends confronted each other, and Storm Shadow revealed that he did not murder his uncle. Despite that fact, Storm Shadow could not totally reconcile with Snake-Eyes. He hoped that after his revenge was carried out, they could be the brothers they always should have been.