Stephanie goes to work with the Coast Guard to help crack an arms-smuggling ring in the area, and becomes attracted to a warrant officer, Scott Daniels, who tries to persuade her to overcome her fear of helicopters after she begins having nightmares of her father being killed in action in a helicopter crash in Vietnam over 25 years ago.
After all the beaches are closed down by Los Angeles budget commissioners looking to cut back on funding for the lifeguard squads of Baywatch. Mitch and the team organises a meeting on the beach with the three budget commissioners and some of the people rescued by the Baywatch lifeguards, they try to convince the city budget official not to stop funding for the lifeguards.
A country-western singer, named Jessie Lee Harris, arrives at Baywatch and after C.J. rescues him from a horde of his fans, he asks her to help him find his estranged wife and son living in the area. C.J.'s newest friend, Sadie, hopes to impress Jessie Lee at an amateur night at the local western club in hopes of wining a spot with his band.
After witnessing a rescue, a bumbling, ambitious TV producer, named Don Brand, decides to make a pilot movie, titled 'Rescue Bay', based on the life of the Baywatch team which results in chaos from everyone after observing their own "characters" in the show, including Garner's look-alike character, C.J. playing Stephanie's role, and Mitch caught in the middle of it all in playing himself.
Matt has a shot at cheaply buying a small yacht and insists Summer should chip and move in. Mitch falls instantly in love with strangely aloof and secretive Kate McCoy. Only after her sudden death is diagnosed poisoning he learns from his cop mate Garner that Kate was an undercover alias of D.C. investigative reporter Catherine Larsen, who found out about secret arms deals.
An attractive wild young woman, named Mattie, and her plain twin sister, Gwen, arrive at the beach and vie for Mitch's affections. But Mitch is unaware that Mattie and Gwen are the same person, a woman with split personalities which soon lands Mitch in danger when Gwen's other personality, Mattie, means him physical harm.
Stephanie, C.J., Matt and Summer take a weekend vacation to San Diego to demonstrate water rescue procedures while staying at the famed Hotel Del Coronado. Summer correctly begins to think that her hotel room is haunted, when she's a haunted by the ghost of a wealthy businessman who mistakes Summer for his lost love from a doomed love affair back in 1943.
Ben Edwards doesn't look forward to a lifeguard reunion of his friends, called the Red Knights, over his walking disability when the rest of them are still fit and active. During a night on the town, Mitch, Ben and the other lifeguard trigger a barroom brawl between the retired lifeguards and a old rival team.
Matt is surprised when his former motorcycle girlfriend Jesse, who is now an aspiring model, arrives to shoot a video for an wave-runner advertisement. At Jesse's urging, Matt helps her discourage the video director's advances towards her and he soon becomes the target for murder by the jealous director, while Summer is struck with jealousy herself after learning of the past Matt had with Jesse.
Olympic champion Mary Lou Retton comes to Baywatch to stage a Special Olympics competition for the mentally disabled. At Mary Lou's urging, Mitch takes under his wing a mentally disabled teen, named Darnell, who tries too hard at winning than on the ethics of the competition. Stephanie befriends Sammy, a shy young girl with Down syndrome who doesn't try at all to believe in herself.
Cort returns to Baywatch, but C.J. is worried there is something wrong with his eyes as evidenced when he bungles a simple rescue by bumping into many beach goers. A beach side attraction where a very tall man works as a "feral man" scares customers is seen by Hobie, who finds the man is a depressed immigrant with no family. Hobie befriends the man, but when he falls in the water by accident his extra large size is a challenge for the Baywatch crew.
Hobie falls in love with a girl in junior lifeguards; Mitch and Jackie have a number of interrupted dates; Matt and Summer discover that they love each other. Thinking he is romantic, Hobie takes the girl on jet ski to a cove near a seaside monastery to kiss her as the bells toll, but they get caught in a dangerous current.