The Ocean team abandons the waters of southern California and journeys north to the rocky, barren Farallon Islands. Under the watchful eye of this National Marine Sanctuary, the crew is the first team ever allowed to hook a great white shark at the Farallon Islands for research. But an unexpected circumstance causes sanctuary observers to temporarily suspend the team’s permit.

On their first day at the Farallon Islands, the Shark Men encounter an unexpected incident with a white shark that causes Sanctuary observers to temporarily suspend the team's permit. For nearly three days, the team anxiously waits to hear from the Sanctuary's Superintendent on whether or not they can resume fishing in this closely protected marine sanctuary.

The mother ship Ocean pulls up off the beach at Malibu. Overhead is a spotter plane looking for shadows. From the plane comes a sighting - shark, 11 o'clock off the port side. With surfers and swimmers in clear view, the Ocean crew gets angling. They are looking to land another great white. The seasoned Shark Men team is back in action - but this time they are close to shore and in the US. After tagging adult great whites off Mexico in Season 1, they now have their sights on the other end of the fish's life cycle - young sharks. Understanding them could help pull together the whole great white story.

The juvenile great white expedition continues off the coast of southern California, where Dr. Domeier and the crew successfully land two juvenile white sharks on the first day of their Malibu expedition. In science, sample-size is vital so the crew continues angling with hopes of catching additional young white sharks. The team hopes to eventually unlock the mystery of how juvenile sharks arrive at adult aggregation sites once they mature.

The Shark Men are headed back to the waters where they have successfully caught and tagged almost a dozen sharks - Guadalupe Island. Dr. Domeier almost has enough data to support his theory about great whites mating at the island. But he still needs a few more blood samples from his primary target - adult females.

The Shark Men have reached their last days at Guadalupe, so they want to make the most of it. They catch one more female great white, Annika, and Dr. Domeier hopes that a blood sample from her will complete his Guadalupe breeding ground research. They also wrangle Apache, a male, a fighter, and their biggest shark to date.