At the Cobra Citadel, Cobra Commander gives more dEMands. Destro discusses with the Baroness that the catalytic elements are low. The Baroness tells him that they've got the upper hand since G.I. Joe failed to get the red crystals. She comments that Major Bludd is still out there and he may succeed in bringing back the crystals.
At the crystal cave mine, Major Bludd has one of the robots modules repaired to go into the mine and deal with any survivors. The robot heads into the mine and breaks through the wall were Snake Eyes is. A glowing Snake Eyes grabs his container of crystals and heads out of the cave. Major Bludd and the Cobra officers ignore Snake Eyes as he's a walking time bomb and will die soon enough.
Out in the ocean on one of the carriers, Doc attempts to probe Duke's mind under hypnosis. Duke sees Selena's face as she is in the slave pens. Steeler announces that they've reached their destination. Breaker points on the grid to let everyone know that the 2nd of the catalytic elements, the heavy water, is in the deepest trench of the ocean. Duke orders everyone to buddy up and to get suited up in their diving gear to go overboard. Stalker asks who is leading the expedition since none of them know anything about deep sea diving. Duke reassures him as Torpedo shows up.
Snake Eyes continues to on with his journey in the snow. He comes up to a cliff edge and it gives way. Snake Eyes falls to the feet of a timber wolf that is caught in a snare. Snake Eyes begins to take off but then returns and releases the wolf. He treks on as the wolf follows him.
The G.I. Joe team prepare themselves as Duke gives them some last minute warnings. Torpedo is the lead since it is his turf and not to get out of their depth suits. Everyone synchronizes with Torpedo as he leads them down into the trench.
As Snake Eyes carries on wearily with the wolf following behind, he meets up with a bear. He attempts to defend himself with the canister but the bear shakes it off. As Snake Eyes pulls his gun to fire, the bear bats him out of the way. The canister flies away from Snake Eyes as he attempts to crawl to his gun. The bear bites his leg and starts to attack as the wolf jumps it.
Snake Eyes again attempts to crawl away but passes out as the wok is thrown near him. As the bear gets ready to attack again, it gets a taser shock from a blind old man. The old man puts Snake Eyes and the wolf on his dog sled and takes off just as the snow avalanches over where they were just at.
At the Cobra Citadel, Major Bludd gives Destro the crystals he obtained in the Arctic. Destro comments that if they get the other remaining elements, no one will be able to stop them and the planet will be theirs.
Meanwhile, Torpedo informs the Joe diving teams to be careful of the surrounding due to the hot fissures. Duke comments about the giant tube worm columns. Torpedo tells them to activate their pressure suits as they head out to the heavy water pool.
Breaker comments about it being a pretty bad neighborhood and Stalker tells him that there's no graffiti as he taps the columns, awakening the giant worms. As the Joe team closes in on the heavy water pool, the Baroness with Cobra officers close in on the area.
The Baroness calls for the attack. Both teams fire back and forth causing more of the giant tube worms to awaken. Torpedo closes in on the pool but one of the Baroness' shots takes out his feet. One of the Cobra underwater ski jet's gets knocked off course into the Baroness' mini sub which then gets turned over.
Torpedo attempts to get the heavy water but the giant tube worms wrap him up along with everyone else. Duke gives permission for Torpedo to make contact with Cobra. Torpedo tells the Baroness that if they are going to get out of this, they'll both have to work together.
The Baroness tells him that it is out of the question but her tank is attacked and she quickly changes her mind but once they're free, they'll be able to split the heavy water equally. Duke agrees with the deal and the Baroness commands the troops to help the G.I. Joe team defeat the tube worms.
As both teams struggle with the tube worms, Duke has them shoot at the base of the columns to loosen their hold of the rocks. As both teams fire on the rocks, the tube worms release both teams and float away.
With Each team getting their fill of the heavy water, the Baroness thanks them for the brief partnership. She pulls her gun and orders them to turn over their supply. Duke says they had a deal as the Baroness retorts that he couldn't be serious to have a deal with Cobra. Each team begins firing on each other as each side retreats back since they got what the needed.
Topside, Duke informs Dr. Vandermeer that they've got the heavy water but they're still short on the other elements. The Dr. tells him that they've got to get the others or it won't matter. Cover Girl relays to Duke that the Cobra Commander demands that G.I. Joe surrender or he'll disintegrate New York City.
Elsewhere, the blind man tells Snake Eyes that the radiation sickness is gone and with some herbs and leaves drew out the contamination. As he pets the wolf, the blind man tells Snake Eyes that his mask and uniform are on the back wall. The blind man comments that he doesn't know why Snake Eyes covers his face but whatever the disfigurement is, he can see that his heart is true and sound. The old man then names the wolf Timber. As Snake Eyes heads out the door, the old man tells him that he'll need the canister that he went back and got for him. He then tells Snake Eyes about an ice boat over the rise that he'll be able to use to get back to civilization.
Back at Joe Headquarters, Dr. Vandermeer tells the team that they're heading in the right direction. Duke tells him that if they give up, Cobra will have a strangle hold over the world and they've got to keep fighting. Short Fuze and Steeler tell Duke that they built a killer satellite with Clutch's help that will knock out the Starr Satellite that Cobra is controlling. Dr. Vandermeer approves of its crude, rough construction.
The killer satellite is put into position and the Doctor launches it. As it nears the relay star, Destro gets a warning alert and calls his shock troops to the grid. Although Destro uses the last of the metallic element, he transports the troopers to defend the satellite. They begin firing on the relay star and destroy it.
Dr. Vandermeer tells the Joe team that they'll have to surrender unless they can pull off a miracle. Just then, the bay doors open with Cover Girl coming in a tank. She tells them she picked someone up on the outer perimeter because she heard a relay alarm while the others where all busy. Up pops Snake Eyes with Timber.
Snake Eyes hands Duke the canister with the red crystals and Scarlett runs up to hug him telling him she knew he was tough to be finished off by the crystals. She kneels and pets Timber as Duke & Dr. Vandermeer isolate the crystals into their MASS Device.
Timber sniffs at the crystal canister and backs away when begins to glow and smoke. Scarlett realizes that it's a booby trap. The Cobra canister spreads its fumes and begins to choke the G.I. Joe team.