There are two separate storylines in this comic, one involving a chase in the Florida Everglades between GI Joe and Cobra and the discovery of Zartan's lair, and the other, the Origin of Snake Eyes.
In the Everglades story. Firefly and Wild Weasel escape from Mutt, Torpedo and Tripwire, who chase after them, attempting to recapture them. Junkyard leads Destro, Baroness, Zartan, and Cobra Commander after the Joes. Or so they think. Junkyard actually leads the Cobras into a pit of quicksand, which they fall into.
In The Pit, Hawk and Scarlett research the meaning of the tattoo that is on both Storm Shadow's and Snake-Eyes' arms, the I-Ching. But they fail to comprehend its meaning. Stalker says that he had seen that tattoo before as well.
He begins the story of Snake-Eyes. Stalker was the leader of a Long Range Reconnaissance Patrol (LRRP) unit in Vietnam. On one mission, they lost three of the six members. Stalker, Snake-Eyes, and Tommy, whose last name is unpronounceable, were the surviving three. Tommy and Snake-Eyes were really close. Tommy always tried to talk Snake-Eyes into joining the "family business" back in Japan after the war. As they were getting extracted by helicopter, they were ambushed. Snake-Eyes was wounded. Tommy went back and carried Snake-Eyes to the helicopter amid heavy Viet Cong fire. As Tommy was pulling Snake-Eyes on board the chopper, that is when Stalker said he first saw that tattoo plus Tommy put Snake Eyes in some kind trance. He saw the tattoo on Tommy's arm. Afterward, Stalker called the Records Division and found that Tommy's unpronounceable last name translated directly into English as Storm Shadow.
Snake-Eyes was then sent home from Vietnam because of his wounds, but no one was there to meet him at the airport. Hawk, who was just a junior officer at the time, was sent to retrieve him and tell him that his mother, father, and twin sister had been killed in car accident by a drunk driver.
In Spanish Harlem, New York City, a young boy walks into a small oriental restaurant and pulls out a gun. The owner, an old Japanese man, plays along with the boy, and calmly yet quickly grabs the gun, drops out the magazine and tosses the boy $50. He claims that he likes to buy empty pistols. The man drops the gun into a box of pistols that he has collected over the years. The whole time, Snake Eyes has been inside the restaurant in disguise, holding onto an uzi. The old man starts a historic tale about Snake-Eyes.
With nothing left in America for Snake-Eyes, he went to Japan to take Tommy up on his offer to join the "family business". This "business" turned out to be a ninja clan. The Hard Master, Tommy's uncle, was the "chairman of the board". The Soft Master, Tommy's other uncle, was "vice-president in charge of finance". And Tommy (Storm Shadow) was called the Young Master. Snake-Eyes undertook the training to become a ninja and excelled. He was eventually allowed to get his arm tattooed with the I-Ching, the symbol of the family. He became superior in most skills, but the Young Master was still superior with the bow. He could even shoot squirrels on the opposite side of a wall with an arrow. Storm Shadow's violent ways became abhorrent to Snake-Eyes, and their friendship weakened. In fact Snake-Eyes became so good, that the Hard Master was going to name Snake-Eyes as the heir to the family business instead of Storm Shadow. The Hard Master was assassinated as an arrow flew through the wall and lodging in a piece of wood, killing him. The arrow is Storm Shadow's and he is seen fleeing the family compound and became the obvious suspect. The Hard Master had actually been imitating Snake-Eyes' heartbeat and breathing in a process called "Donning the Chameleon's Mantle". So that meant that Snake-Eyes was the actual target. This made Storm Shadow even more of a suspect because it was assumed that he became jealous of Snake-Eyes and wanted to kill him. As he died, he claimed that Storm Shadow was innocent, yet all evidence pointed to him. The future Cobra even fled the family business.
In the Everglades, Destro has stopped Zartan from shooting Junkyard. He wants to see why a dog is alone out in a swamp and staring out into the trees. The Joe team is out in those trees, angry that Junkyard is giving them away.
