During the first week of autumn at Baywatch with Hobie gone away to college and heavy rainfall in the area, Mitch discovers that his shipboard marriage to Neely is invalid, which worsens things then Neely's ex-husband suddenly shows up with no knowledge of Neely's baby or anything else making Mitch realise that Neely lied to him all this time and she has fully reverted back to her conniving and devious true self.
Mitch, Craig, Neely, J.D. and Newman co-operate with the Coast Guard in rescuing as many people as possible from the waters of the plane crash and fending off shark attacks as well.
Mitch deals with Captain Alexis "Alex" Ryker, the conniving CEO of a private lifeguard company called Bayguard, who wants to take over the Baywatch lifeguard company to expand her company. When Mitch suspects Alex of setting up rescues to appease Chief Johnson, he resorts to having Cody spy on the Bayguard team to uncover any underhandedness.
Cody accompanies Alex on a vacation to Hawaii where she wants to spend time with her autistic 10-year-old nephew, Timmy, and to show him to swim with dolphins in the local lagoon, which the mute Timmy is afraid to do so.
A mysterious figure called "The Phantom Lifeguard," begins making rescues and disappears before being identified by anyone. While Mitch thinks the Phantom Lifeguard is an outsider, Cody and J.D. think the unseen hero of the day is getting his/her information from inside the department.
April mentally falls apart after losing a rescue, while Mitch and the grieving widow refuse to give up searching for the body.
Hobie takes out his wild and crazy college friends for a boat trip while under the influence of alcohol and they all end up in a boating accident in which Hobie's girlfriend falls into a coma and leads to Hobie being arrested and facing charges of manslaughter.
Mitch befriends Tanner, an abused nine-year old boy who tries out for the junior lifeguards in order to get away from his ill-tempered, alcoholic, divorced father, Blake. But Mitch feels helpless in helping Tanner when everyone tells Mitch not to get involved in the boy's troubled home life and to mind his own business. Things turn chaotic when a bus falls off a bridge and lands in 20 feet of water.
Mitch, feeling that his life has reached a midpoint from his failed marriage to the absent Neely, goes for a day-long tower swim along the beach and encounters various other problems which include, April and Craig's growing attraction for one another, and reluctant heroes Cody and J.D. refusing to take the credit for saving two girls and a pair of policemen after falling off a pier.
Mitch takes in an orangutan, named Morton, that escapes from it's abusive dwarf owner which complicates Mitch's and Alex's plans for Baywatch's annual Special Olympics program, while Cody and Jessie deal with Morton's owner, Herbert Green. One of the Special Olympics participators, a hearing-impaired girl named Kara, takes a liking to Morton and when she tries to hide Morton from Herbert, they end up trapped in a cave with a rising tide that threatens to drown her and the orangutan.
Cody puts his career (and life) on the line when he starts using a performance-enhancing supplement in hopes of making it to the 2000 Sydney Olympics, which soon begins affecting his life guarding job as well.
Mitch becomes acquainted with some old armed service friends of an Army parachutist team where he tries to reunite one sky jumper, Tracy McComb, with her estranged Naval officer father who has a terminal illness. Jessie becomes intrigued with skydiving and persuades Mitch to go along with her for a jump, which takes a turn when they are forced to rescue some people from a boat wreck off Catalina.
Mitch finds himself on the wrong side of the law when he becomes reacquainted with Tanner, the abused nine-year-old boy, whom he snatches away from his abusive father, Blake, and lets the boy stay at his house while Alex becomes Mitch's co-conspirator in helping Tanner.
Craig tells Mitch a shocking secret that he has lymphoma when they become caught up in a high-risk adventure at sea starting when they get lost in a fog while paddle boarding and then get attacked by a shark. They manage to reach land only to end up as prisoners on a top secret military test range. Back at Baywatch, April cannot find the right time to tell Manny about her involvement with Craig.
Mitch gets the need for speed when Tanner's cousin Damon Lusk, a race car driver, visits for a race car competition, and who also has a meeting of the minds with Alex. But when Damon falls ill due to food poisoning, he asks Mitch to take his place for a major grand prix race, where Mitch comes up against an old rival from his own former race car days.
Mitch's Zuma Beach lifeguard friend, Jake Barnes, learns that his Australian ex-wife has suddenly died. So he, Mitch, Alex, April, Cody, and Jessie go on a trip to Australia where Jake is to meet the eight-year-old son, Terry, that he never knew. Upon arrival, Jake with Jessie in tow, travel to the Avalon Beach Resort Club where Jake meets with Terry and his ex-wife's friend Allie Reese, a helicopter pilot and lifeguard at the beach club, where Jake and Terry seem to hit it off.
While Mitch, Alex, Cody, and April prepare for their race against the Australian lifeguards, Jake must choose between staying in Australia with Terry or returning home without him. But when Terry does not want to leave Australia, he goes missing which prompts Jake, Jessie, and Allie to look for him.
Having received a Dear John-type letter from Lani saying that she has moved on and is now romantically involved with someone else in New York, Cody gets a lesson in love when he and Mitch help out a brilliant, but troubled, violinist named Ariana to get away from Lena, her dangerous and overbearing trainer with a secret agenda.
While on her way to her grandmother's birthday party, Alex's day gets sidetracked when she tries to save a diamond runner, named Ben, whose partners, Lisa and Jason, want to silence him for good which leads to a standoff in an underwater cave with Alex and Ben trying to avoid the rising tide and the smugglers circling above in their motorboat.
April tries to save Manny from himself after he suffers a life-altering back injury during a rescue. April then decides to take Manny's place with Hobie in a boat race with the other lifeguards from Baywatch.
April and Jessie search for the perfect celebrity host the Miss Galaxy Beauty contest Baywatch is sponsoring, when they stumble across and get duped by a con artist impersonator, called Earl, who claims to be the real George Hamilton.
A frantic weekend begins for Alex when she begins tracking down the builder of several elaborate sand castles that appear every day at the beach, while she gets stuck entertaining her life-long childhood friend Sam's fiance, Diana, who falls for Mitch, which prompts Mitch to asks Alex to pose as his girlfriend to keep Diana away.
