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Picking up where we left off last issue, being stuck in quicksand thanks to the G.I.Joe dog Mutt, Baroness and Zartan fire at him and Destro and Cobra Commander watch. Meanwhile the Joes Mutt, Torpedo and Trip wire hear the shots and Junkyard needs reassured that Junkyard won't get hurt. Meahwhile up ahead Firefly makes a Maylan tiger gate trap for the Joes. Destro in quicksand fires a wrist rocket at a tree and he and the others get out of the quicksand meanwhile Junkyard runs into the Joes and appears to have hit the trap with a twang.
Back at the Pit, Scarlet, Hawk, and Stalker continue talking about Snake Eyes. Hawk and Stalker were getting the Joe team assembled and set to recruit Snake Eyes who was now living in the high Sierra's. Scarlet now continues the story. She met Snake Eyes while she was training the guys in hand to hand combat. She took the recruits down and to save face and her dignity, Snake Eyes let her throw him and she sensed that. Feeling fascinated by him, she and him started talking on a ferry but she was tiffed that he liked her due to her resemblence of his sister. It is revealed in this part that she liked him.
The story continues. On manuevers in a helicopter that was going down due to sandgetting in the copter Scarlett became stuck. Snake Eyes goes back to save her and the gas main blew up in his face like a box of roman candles. He saved her but with dire complications, his face severly burned and the loss of his voice. He could have had complete disability but Snake Eyes stays. Back in Florida Junkyard pulled the trigger but is ok. The Joes go to take back Wild Weasel and Firefly back as prisoners but the rest of Cobra down there start a fire fight.
Back in Harlem, the Soft Master is still talking to Snake Eyes and tells him he decided to come looking into the killer of the hard master and bring him or her to his justice. Continueing on with his back to the window, Soft Master knows that Storm Shadow is there and tells Snake Eyes to get him and Snake Eyes shoots the window out. Storm Shadow comes flying in and retrieves his arrow that killed his uncle all those years ago. Thinking he is trapped, Snake Eyes shoot the counter but Storm Shadow escapes through the hidden cellar door. The police arrive but Snake-eyes and Storm Shadow are both gone with Snake Eyes on the pursuit of Storm Shadow. Back at the Pit, Scarlet intercepts a police report of a masked man with an uzi fighting a white ninja. Snake Eyes and Storm continue the cat and mouse onto the train tracks and onto a train.Of course the Joes from the Pit make their way to where the fight is at. On the train Storm Shadow finally figured out that was Snake Eyes he fought at Castle Destro back in the infamous silent issue #21. Still on the train we learn Storm Shadow has no grudge against Snake Eyes and he loves him like a brother, but he will not let Snake Eyes stand in his way of what he needs to do. Storm Shadow is unaware the tunnel is coming and thinks that Snake Eyes wants him to attack. But Snake Eyes saves Storm Shadow by doing that and a debt is repayed. Storm Shadow proceeds to tell Snake Eyes he did not kill his uncle that a mysterious person in a ZCobra small copter did it. Storm joined Cobra to find the killer and once the day comes, perhaps they can be brothers again..