|“||I am the greatest ninja in the world, and I will make sure Snake-Eyes knows this with his last breath.||”|
—Storm Shadow is eager for a family reunion.
Storm Shadow hungers to be the greatest ninja in the world, and the only person standing in his way is Snake-Eyes. As a young man in the Arashikage ninja school, Storm Shadow demanded that his uncle teach him the final step in the Seven Steps to the Sun, a ninja technique of immense power. But his uncle refused to do so, questioning his nephew's worthiness. Now, Storm Shadow has instigated a showdown to prove that he is a greater ninja than Snake Eyes - and by proving that, he will also prove that he was the most favored student in his uncle's eyes.
|“||You're a lot better than I expected... but you still don't want to cross blades with a ninja!||”|
—Storm Shadow, trying to intimidate Tunnel Rat by being conceited...
Storm Shadow infiltrated the U.S.S. Flagg on a mission to set explosives, but was discovered and confronted by Tunnel Rat. The two fought to a draw in the bowels of the ship, and Storm Shadow was forced to retreat. Storm Shadow admitted that Tunnel Rat was more of a worthy opponent than he anticipated, aware that he had deactivated his bombs in time..
|“||Your friend is more ready than you. Violence is a burden to him; to you, it is less than air.||”|
—Hard Master, contrasting Snake-Eyes' responsibility and Storm Shadow's homicidal tendencies.
Tommy Arashikage grew up under the ninja training of his uncle, the Hard Master, apparently training and learning ever since he could first walk. The most significant technique ever learned by any student was called the Seven Steps to the Sun, the martial art Hard Master created and founded the reputation of his ninja school upon. Eventually, the boy who would later be known as Snake-Eyes came to learn from the school founded by Storm Shadow's uncle. Storm Shadow and Snake-Eyes rivaled each other in swordsmanship skills, but became best friends and sword brothers. Snake-Eyes had come to learn at an older age than Storm Shadow, and therefore needed private training apart from the other students to keep up with him. Both Snake-Eyes and Storm Shadow, being the more skilled students, were taught some of the Seven Steps, Storm Shadow being taught up to the sixth and Snake-Eyes up to the fifth. Unknown to Storm Shadow, however, Snake-Eyes proved himself worthy and was taught the Seventh Step secretly at some point.
While training with the other Arashikage one day, Storm Shadow broke off to speak with the Hard Master, addressing him as "uncle" rather than "sensei," despite the other students still being present. After briefly discussing Snake-Eyes' private training, Storm Shadow demanded to know why his uncle would not finishing teaching him the Seven Steps to the Sun. The Hard Master told him that passing on the knowledge to utterly destroy with merely seven blows was passing on "a responsibility like no other." Storm Shadow said that the Hard Master needed to pass on all Seven Steps, as he would not live forever and the "soul" of his school needed to survive. Hard Master pointed out that death was not the only thing he had to teach, and said that Snake-Eyes was more ready, as violence was a burden to him, but to Storm Shadow, it was "less than air." Dismissing Storm Shadow's anger, he ultimately said he would not teach him the Seventh Step and casually walked away.
A sniper was positioned on a cliff above the training grounds, hiding with a rifle. Storm Shadow removed his neck cloth and threw it in the air, signaling the sniper to fire. Snake-Eyes realized what was happening, and ran to save his sensei. The sniper first shot at him, putting a bullet in his jaw. Then, as Hard Master turned around, a bullet went straight through his head, killing him. Storm Shadow said to Snake-Eyes that "it had to be done" and that they could now truly become ninja and make the school into what it should be. Furious at Tommy's betrayal, Snake-Eyes drew his sword and challenged his best friend. Storm Shadow said that vendetta would be called for if Snake-Eyes struck another Arashikage, to no avail. The fight was short, and Snake-Eyes fled the compound after knocking Storm Shadow to the ground and making his mouth bleed. Storm Shadow just smiled, knowing he would get the chance to fight him again.
U.S.S. Flagg Sabotage
|“||Storm Shadow killed Bazooka, sabotaged the armory, and now, he's calling you out.||”|
—Duke, at this point, being Captain Obvious to Snake-Eyes.
Storm Shadow would become a prominent member of the powerful organization with the goal of world domination: Cobra, serving under Cobra Commander. He successfully sabotaged the U.S.S. Flagg, greatly damaging the G.I. Joes' armory. While onboard, Storm Shadow also encountered Bazooka, killing him.  In the throat of Bazooka's corpse, Storm Shadow left a small rolled up paper with the Arashikage symbol. Hidden on the paper was a message saying "All games end today. Meet me where we first played," visible only under an infrared light.
When Bazooka's body was examined by the Joes, Snake-Eyes deciphered the message and was given permission by Duke to go and confront his nemesis at the Arashikage training compound. Likewise, Storm Shadow was allowed by Cobra Commander to go to the compound, given a detachment of Cobra Troopers as backup. As the commando infiltrated the island and dispatched the troopers waiting there, Storm Shadow watched from a concealed position on one of the island's mountains. When Snake-Eyes reached the training grounds, Storm Shadow approached him from behind, ready to commence their final duel, and repeated his note's statement: "All games end today."
|“||I hate you because he chose you. That's all. I had him killed by a Cobra sniper, but you? All I've wanted for years is to kill you myself!||”|
—Storm Shadow giving insult right before adding injury. Harsh.
Storm Shadow gave a speech about how he truly hated Snake-Eyes and never cared about vendetta after their first fight, showing that unlike he had said all those years, he never stood for honor and had become corrupted in his anger that the Hard Master would not teach him the Seven Steps to the Sun, but would teach Snake-Eyes. The two then began a furious dual by swiftly lunging at one another. The fight between the two went on, and towards the end of the fight, even after losing both his swords, Storm Shadow blocked Snake-Eye's attempt at using the Fifth Step to the Sun. He said that Hard Master hadn't taught Storm Shadow the seventh, but didn't teach Snake-Eyes the sixth. He then used the sixth step to knock Snake-Eyes into a building.
As the dust cleared, Storm Shadow found Snake-Eyes had recovered and was coming up behind him. He then barraged Storm Shadow with several well placed jabs to his limbs, disarming him and causing him to kneel at his mercy. Storm Shadow looked up at Snake-Eyes and realized that Hard Master had managed to teach all seven steps to Snake-Eyes, the truly worthy student. Snake-Eyes' knuckled palm then came towards his forehead. On impact, the final blow seemed to cause Storm Shadow's brain to implode. He then moaned sadly at the shocking revelation, and collapsed on the ground, defeated and apparently dead. Snake-Eyes gave Tommy a proper burial on a mountain outside the training ground and looked over his fallen friend, before leaving.
However, the epilogue again showed the grave site... empty. Storm Shadow's current status remains a mystery.
- This version of Storm Shadow is 100% villain, following no code of honor, ninja or otherwise.