In the Caucasas Mountains in the former Soviet Union, some soldiers are digging up a block of ice. They are told to be careful with it, because last time the man in the ice was loose, he almost split the nation in two, in less than a week.

Omega Red wakes up in a military base all chained up. Through a monitor, a man wants to make him a deal. Omega Red says he doesn’t deal with imperialists, that he was made to fight them. The man says that that war is over, won by them. The man promises to make him human again if he goes with the deal; he needs to clean up a sunken nuclear submarine near Pearl Harbor. The officer explains that Omega Red is the one suited for the job, because he knows the codes of the former government and can resist any kind of radiation. He also warns Omega Red that he had his scientists implant a vile of nitrogen in Omega Red, so that they can kill him if he betrays them. Omega Red goes along with the deal, but only if he gets two companions on the mission: Wolverine and Storm.

Xavier explains the situation to his X-men, and threatens Wolverine to take his place as Omega Red’s hostage when he opposes the plan. Wolverine decides to go. Storm and Wolverine are about to board a submarine with Omega Red, when Wolverine almost gets into a fight with him. Asking Logan to calm down, Storm holds him back.

Storm navigates the mini-submarine towards the wreck. Omega Red explains he will have his humanity back, while Wolverine will never regain it. This angers Wolverine, but Storm asks him to stay calm, because narrow spaces make her ill. They land on the sunken submarine, and after Omega Red is released from his shackles, they board it. Wolverine and Storm wear suits protecting them from the radiation. Omega Red enters the codes into the computer, and reactivates the reactor. He starts the submarine, and the colonel contacts them to say that they must take the submarine home. Omega Red refuses and takes out the vile of nitrogen with one of his tentacles. Wolverine wants to attack immediately, but Storm reminds him of the fact that Omega Red need only to tear their suits apart to stop them, and that Wolverine might survive, because of his healing factor, but she would be killed.

The colonel contacts the navy at Pearl Harbor.

Wolverine can’t take it any longer, to see Omega Red with a dangerous weapon like the ship and it’s missiles and shifts his claws out, tearing his gloves apart. He attacks Omega Red. Omega Red throws Wolverine off him with his tentacles. As he approaches Storm and Wolverine, Storm blows him to the ceiling with her winds. Wolverine’s lungs are almost immediately intoxicated, and Storm supports him while they try to escape to the mini-submarine. Omega Red captures them with his tentacles when they are almost there. Omega Red says through the com-link with the colonel that he has programmed the missiles to destroy the 15 largest cities in the world and that all he wants to do is watch them burn.

Beast and Rogue are in the Blackbird above the sea, and Xavier tells them through the com-link that the Navy’s are on their way, after making sure the depth charges are programmed correctly.

In the submarine, Storm tries to find out Omega Red’s motives. They suddenly feel an explosion, and Omega Red wonders how the army got there so quickly.

The Colonel registers the depth charge of the Blackbird, but doesn’t register the Blackbird itself, as it is invisible to the radar. Omega Red is about to launch the missiles when the Blackbird makes some more depth charges. The submarine shakes and Omega Red falls to the floor, releasing Wolverine and Storm from his tentacles. Storm is trying to get away, but one of Omega Red’s tentacles tackles her. She throws lightning at him.

A Weapon Expert explains to the Colonel that there might be a warhead override, so his team can take out the sub’s weapons. Normally the missiles don’t arm until near their targets, but that Omega Red might have reprogrammed it.

Beast notifies the Professor that Omega Red has reached launch depth. Xavier advises to stall him as long as they can. However, it’s too late, Omega Red has launched the missiles. Rogue takes out one of the missiles with the blaster of the Blackbird and there is a small explosion, following the shot. Beast says that the missiles are still in pre-armed mode, so Rogue is free to take out all of the other missiles.

Meanwhile on the submarine, Omega Red figures out that the Navy could never have been that fast, and that it must have been the X-men. He wraps Storm up in a lead pipe. He warns the Colonel that if someone fires on the missiles again, that the Hawaiian coast will be history. Rogue is fed up with Omega Red, and dives from the plane into the water. She bends the submarine bare-handedly so that it can’t move and can’t fire missiles again. Storm takes Wolverine to the mini-submarine. The submarine is attached to the Blackbird with ropes, and they take off.

Storm and Wolverine wonder if Omega Red might still be alive. Down in the large submarine, Omega Red tries to start the engine again, but the navigation fails and the ship takes him into the depths of the ocean.

In Xavier’s office, Beast tells the Professor that Storm’s claustrophobia will pass, but that he isn’t sure whether Wolverine will be okay with the possibility that Omega Red is still alive.

On the bottom of the ocean in the submarine, Omega Red opens his eyes.