After weeks of searching, the Sea Shepherds finally spot a Japanese whaling ship, the harpoon vessel Yushin Maru #2. Captain Paul Watson devises a dangerous plan for two of his crewmembers to board the vessel and deliver a letter telling them to stop the killing of whales. He hopes to create an international incident, but his plan sparks a safety debate that divides the crew. Two volunteers enlist for the mission - Ben Potts and Giles Lane - and the crew braces for the worst as the men jump over the railing of the enemy ship. They are immediately tied up by the Japanese fishermen, and the Yushin speeds away with the two Shepherds still aboard.

With Ben and Giles of Sea Shepherd being held hostage aboard the Japanese whaling ship Yushin Maru #2, Captain Paul Watson is pleased at the international media storm he has created, and rejects an offer from whalers to release the hostages.

After three long days, Pottsy and Giles are transferred back from the Yushin Maru and become instant celebrities with the media. Just as they are settling back in, the crew is concerned when they discover an unknown ship has been following them! The Captain plans a surprise recon on the mystery ship to determine its intentions. The Delta and Helicopter are launched together in order to ambush the vessel and they discover it's a spy ship for the Japanese whalers. Paul persuades his crew to attack the spy ship, but just as the Delta boat is preparing to launch, a crucial tool on the Steve Irwin breaks - the hydraulic crane. Not only is the attack aborted, but the whole Sea Shepherd's mission is in jeopardy.

The ship's engineer reports that one of two engines is broken. Now they will be unable to keep up with the Japanese whalers and are forced to return to Melbourne for repairs. While heading back, they are forced to navigate through a massive oceanic storm size of Australia. After they make it out alive, the crew throws a party to celebrate but the officers are angry and order the Steve Irwin to now become a dry ship. This is the final straw for many volunteers and they decide to get off the ship when they dock. With astronomical engine repair costs and a skeleton crew, the Sea Shepherds are worried they won't be able to raise enough money to complete their anti-whaling campaign.

Armed with new volunteers, the Sea Shepherds head out to sea to find the Japanese whaling ships. After they pinpoint the fleet's location, the Captain raises the stakes and plans for another boarding. This time it will be an all-female boarding team!

The Sea Shepherds have finally found the most important ship in the Japanese whaling fleet, the Nisshin Maru factory ship. Everything has led to this moment and despite warnings from the Japanese whalers, the Sea Shepherds strike. After two rounds of attacks, the Japanese whalers retaliate with concussion grenades. During the battle, the Captain claims to be shot and he removes a bullet lodged in his bulletproof vest, aimed at his heart. The Sea Shepherds alert the media that Paul Watson is safe and triumphantly depart Antarctica. They claim to have successfully saved hundreds of whales but know their mission will never be over till whales are no longer being slaughtered in the Southern Oceans.