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.

In the Season 5 premiere, the Sea Shepherd Conservation Society responds to Japan's 2011 announcement to resume its whaling operations in the Antarctic and the government's promise to beef up the fleet's security.

A plan to intercept the whaling fleet before it reaches the whaling grounds is nearing a critical point. The new helicopter pilot, Gary, spots a ship on the horizon; If it is the whalers' factory ship, this may be Sea Sheparhd's the earliest victory ever.

The Sea Shepherds' scout vessel, the Brigitte Bardot is damaged by a 30-foot wave, and help is more than 20 hours away.

With the Japanese fleet's security vessel looming on the horizon, the captain of the badly damaged Brigitte Bardot orders his crew to evacuate the boat. Meanwhile, in Antarctica, the Bob Barker deploys the small boats team to disable a harpoon ship.

The exhausted crew of the Brigitte Bardot scramble to evacuate the ailing vessel. And Captain Paul Watson goes on the offensive, sending a team to board the heavily armed security vessel: the Shonan Maru.

With three activists aboard the Japanese security vessel, Capt Paul Watson hopes the media frenzy will force the Shonan Maru 2 to back off. Meanwhile, the crew of the Steve Irwin are plunged into their most violent battle yet.

When a massive target is detected on their radar, Sea Shepherd sends out their new helicopter pilot to ID the mystery vessel. But as the helicopter reaches the limits of its fuel range, it abruptly disappears, crashing into radio silence.

After months of frustration, Sea Shepherd finally find their target - the Nisshin Maru. Now, they must run an eight-mile gauntlet blocked by two harpoon ships aggressively defending their mother ship. The success of the campaign rides on this moment.

The Sea Shepherds face a difficult 2013 campaign with the Brigitte Bardot and their helicopter unavailable. The fleet introduces a new ship, the Sam Simon. Former captain of the Steve Irwin, Paul Watson, is forced to step down due to an injunction preventing him from coming within 500 yards of Japanese whaling fleet. All four of the fleet's main ships feature a new captain, with Watson serving as an observer. The Steve Irwin remains to coordinate the operation. The Bob Barker is sent to search for the whaling fleet and finally locates the Nisshin Maru near the western edge of the whaling ground. However, they sit helplessly as the Japanese successfully kill and load a whale onto the factory ship. The Sam Simon is sent to search for the bunker ship Sun Laurel and finally locates it along with 2 Japanese whaling ships. They attempt to block the refueling, but fail when the rookie captain pulls away, not willing to risk his crew. After hunting, the Nisshin Maru turns east. Realizing that the factory ship is trying to also refuel, the Sea Shepherds send all their ships to interfere. 30 hours later, the ships prepare for the showdown. The 500-tons Bob Barker blocks the 5000-tons Nisshin Maru by parking right next to the Sun Laurel. The Japanese warns the Bob Barker to move but captain Peter Hammarstedt refuses to comply. The Nisshin Maru then pushes the Bob Barker with their bow, damaging the ship and causing it to list dangerously. After a standoff, the Nisshin Maru backs away while the Sun Laurel abandons the operation. Days later, the whaling fleet leaves for Japan with only 103 kills.