Season 1

Paul Watson is allegedly shot by the Japanese whaling crew during a confrontation between the whaling factory ship Nisshin Maru and the Sea Shepherd vessel MV Steve Irwin. The episode then flashes back to the maiden launching and departure of the vessel from homeport three months earlier.

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 crew members 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.

Without negotiation and confrontation with the MV Steve Irwin, the Yushin Maru № 2 agreed to transfer Pottsy and Giles to a government ship that would then meet with the Steve Irwin at a rendezvous point to return the two members. 1st Mate Peter Brown decides to launch an attack on the Yushin Maru № 2 at dusk. Four crewmembers are sent on the Zodiac inflatable boat Delta to carry out the risky mission. After losing radio contact with them, recon pilot Chris Aultman, who was sent too late to survey the situation, reports that they are heading in the wrong direction and must return as night falls. The lone Delta was feared to be forever lost out in the middle of the dark, frigid, vast Antarctic Ocean. Fortunately, contact was finally made with the Delta, which eventually returns to the MV Steve Irwin over two hours later and behind schedule to retrieve Pottsy and Giles.

Giles Lane and Ben Potts safely return to the MV Steve Irwin. The crew then discovers that an unknown ship, allegedly spying for the Japanese whaling fleet, has been following them, decides to recon it from behind a tabletop iceberg for any military personnel aboard, and temporarily drives it away after seeing no sign of illegal military activity. The crew later plans to ambush the mystery ship, soon identified as the Fukuyoshi № 68, to prevent information about the Steve Irwin's whereabouts from being given to the rest of the whaling fleet. They plan to do this by boarding the vessel and sabotaging its communication equipment, shutting off any communication with anyone. Before the mission, a hydraulic crane used to launch the motor rafts somehow got damaged, jeopardizing the Sea Shepherd's mission.

The MV Steve Irwin experiences several technical difficulties, including a damaged engine, hydraulic crane, and helicopter. Running on only one engine, the ship must return to port at Melbourne, Australia to make repairs while the whaling continues. Some crewmembers decide to party and leave the operation. Upon arrival, they were welcomely greeted and cheered by the citizens, and by the police. Pottsy and Giles become instant celebrities on homecoming. After recruiting new members, the crew travels without its recon chopper and returns to the Southern Ocean only to find that the suspicious ship is still following them.

After noticing that the suspicious ship Fukuyoshi Maru № 68 has found and followed the MV Steve Irwin again, Watson unsuccessfully attempts to send four female crewmembers to board the vessel to deliver a warrant. This leads to a man's injured thumb and a woman's injured pelvis (Incidents not related). The Steve Irwin detects the Nisshin Maru on radar. At dusk, the entire ship experiences a power outage, leaving it drifting through an iceberg field without operating engines.

After power was restored to part of the ship, the MV Steve Irwin finally finds, follows, and comes face to face two times with the Japanese whaling factory ship Nisshin Maru, which Watson considers the "most evil" vessel in international waters. A pod of whales swims between the two "warring" ships, which eventually engage in a ship-to-ship "battle." The captain of the Nisshin Maru warned on a recorded message sent multiple times through a horn that "If you dare board this vessel, you will be taken into custody." Recruited Sea Shepherds are the first to strike, throwing stink bombs with Butyric acid onto the decks of the Nisshin Maru, which dwarfed the Steve Irwin in size, while its crew watches and films the Steve Irwin. The Japanese whalers claim that three of their crewmembers were injured by the stink bombs. When the two ships meet the second time, the Steve Irwin crew strikes first again while the Nisshin Maru crew, in return, threatens to use tear gas grenades and throws flash bombs. Watson fishes a metallic fragment from his vest and claims to have been shot. As Watson concluded that the second leg of the mission was successful, the Sea Shepherds claimed that they have saved about 500 whales. The Steve Irwin returns to Melbourne again before running out of fuel.