Sean faces a major life-changing decision to leave for Australia or stay with Baywatch Hawaii, while Leigh has agreed to marry Sean in a wedding ceremony on the beach.

Sean has his hands full in dealing with Jena who wants to close down the training center to make room for a group of crooked investors looking to turn the Oahu North Shore into a hotel chain. So, Leigh tries getting Erica, a British entrepreneur to be the Baywatch Hawaii sponsor in order to keep the training center open, but with complications whom she makes advances to Sean.

A new computer is installed at Baywatch headquarters but could spell disaster if it is not working properly before a sponsor's visit.

Sean becomes concerned over Leigh's new boyfriend Sam Parks, an air plane pilot who thrives on living dangerously, and whom takes her out on a hand gliding trip headed for disaster.

Sean, J.D. and Kekoa travel to the Big Island to help with the extra work caused by the Ironman Triathlon. They soon have a run-in with former lifeguard Jessie Owens, who is also competing in the Triathlon and has new infant son with her. This causes some awkwardness in J.D., and slight jealousy in Kekoa who suspects that J.D. never got over her.

During the training sessions for new Baywatch Hawaii lifeguards, Sean deals with Jena and other Hawaiian officials who don't see the training center as a profit making enterprise. During a drive, Sean accidentally hits into Zack McEwen, a new recruit and surfer from Michigan who joins the training team while Jason becomes acquainted with Carrie Sharp, one of the rookies from San Diego who finds him irresistible.

After Danny gets into trouble again with the law, Sean gives him a choice of being arrested or joining the training center team. Danny reluctantly joins the rookie team, much to Leigh chagrin who openly admits that she does not trust Danny, while Jenna continues her mind games by trying to recruit Leigh under her wing.

Leigh and Sean become entangled in a dangerous position when he suspects an attractive tourist, named Sasha, of murdering her husband, but cannot prove it to anyone.

Sean deals with a series of prank phone calls for non-existent rescues and discover that McKenna's son is one of those responsible in which Jenna uses this to try to heat up the war between McKenna and Sean into a lawsuit hoping McKenna will finally close down the Baywatch Training Center. Zack deals with a slight hearing loss in one of the rescues while dealing with Jenna trying to get his help to bring down McKenna, while Zack is showing around Peggy, a prospective new trainee.

Sean and Leigh land in mortal danger after they rescue two surfers off a reef at Maui where one falls ill, and Sean becomes suspicious to the cause which may be connected to the reef. During their investigation of a local company, they end up as captives by the corrupt department head to cover up them using toxic chemicals to create a man-made reef.

Sean, Jason, and Zack travel to the Big Island to participate in the Showdown 2001, a 12-mile course of natural obstacles. Leigh will be taking over supervisory duties at Baywatch while Sean is away. J.D. is tending to Kekoa, who has come down with the flu. Fortunately, J.D. has an iron constitution, despite the fact that he didn't have his annual flu shot.

A typical day begins when Kekoa deals with three rescues simultaneously one of which involve a brash and spoiled teenage wave runner who causes accidents in the area in which his equally spoiled and arrogant father threatens to sue the team for not coming to his aid in time.

Sean deals with Blake, a nefarious "shark tour" provider who dumps chum bait in order to lure dangerous sharks to the area for tourists to see from underwater shark cages causing the beaches to become dangerous with the sharks in the area.

Sean struggles with his inner demons after a teenage friend, named Mike, dies during a surfboarding outing which a frustrated Sean Patle boards out in the ocean, runs into a rain squall where stranded in the ocean he has visions of the people in his life and of his own long dead son Ben.

Carrie's life turns upside down when after she and Leigh save two spear fishermen from drowning, after which one of them asks her out on a date in which he begins stalking her and wanting to control her.

A bad week begins once again for Sean when two frivolous lawsuits, one by Kekoa's father over nearly drowning at the beach, and another by an equally wealthy man thinking that he lost his gold Rolex wristwatch. The local city council, now with Jenna on the staff, seeks another chance to try to close down the training center, in which an attractive special investigator, named Jackie Love, arrives to check up on Sean's work.

Jenna gets taken in by a fast-talking con man, named Lyle Garrett, who claims to be an investment banker who wants her money for a quick IPO investment, despite Sean's suspicions who sees through Lyle's charade.

Sean rescues a local TV celebrity who is in trouble with his kayak. This brings the team a lot of media attention, and because Sean turns down the offer of a TV interview, he is offered a week at the Hilton Hotel. Sean, though, does not like to take freebies either so he declines. But Zack gets an idea of his own: he will take advantage of the freebie vacation Sean was offered at the Hilton Hawaiian Village by pretending to be Sean!

Jason becomes smitten with Maya Morgan, a young volleyball player and an old childhood friend of Carrie's and thinks that he's found the girl of his dreams, never imagining that Maya is dying from a heart disorder unless he gets a heart transplant.

Jenna intensifies her personal war against Sean by confiscating some of the team's equipment, including a Scarab, and trying to get her boss McKenna, a ruthless and greedy local councilman, to close down the Baywatch Hawaii training center.

Zack becomes devastated when Sean refuses to promote him to a full-time lifeguard due to his brash and reckless attitude after rashly trying to capture a purse snatcher on the beach, in which Sean gives the promotion to Carrie instead.

A major hurricane hits the Hawaiian islands in which Sean is trapped with Jenna in a underground bunker which rising flood waters threaten to drown both of them unless they put aside their personal conflicts and hatred of each other to survive the day and night.