28 Aug. 1999Wreck of the Zephyr
Tom Hampton's 17-year-old niece, Courtney runs away from home after a row with her mother and shows up at Tom's house unannounced. Tom tries to patch up the relationship between Courtney and her mother, Sarah, but it takes a shipwreck which nearly kills the older woman for Courtney to realize how much she loves her mom.
16 Oct. 1999Blind Faith
Tom blames himself for the death of a man during a failed rescue attempt. He suffers a crisis of confidence and his family rally around him in support. Tom's moment of truth comes when he is once again called on to save somebody. The rescue is successful, and Tom's faith in himself is restored.
18 Sep. 1999The Wish
Jackie and Courtney befriends a little girl named Shelby. They have plans for Shelby to swim with flipper. However, Shelby's mother Jean is reluctant to let Shelby play or be out of her sight because her little daughter has leukemia. Alex and Jean become good friends. They all learn that Shelby's 'wish' is to be able to swim with flipper. Meanwhile, Chris thinks his little league team has a good chance to win a rival game and make it to the state championship because of Tom, his father's outstanding coaching skills.
Tom takes Chris diving on his 12th birthday, but has to go on a rescue soon after. Tom develops the bends because his helicopter has to fly at 20,000 feet to get over a storm. Tom is taken to a hospital, where he spends a few hours in a re-pressurization chamber. After getting out of the hospital, he is put on leave for a few days but is hanging around Search and Rescue when a call comes in about a trapped diver. Off he goes, even though he is not fully recovered.
Chris gets his first job delivering papers. On the first day, he crashes his bike into a gate belonging to an elderly man. Chris discovers that the man's son died in a boating accident five years earlier. He befriends the grieving father and helps him come to terms with his loss.
4 Dec. 1999Free Diving
Champion free-driver, Stephanie, will do anything to break the world free-driving record, including risking her life. Tom and Flipper race to the rescue when Stephanie lapses into unconsciousness hundreds of feet under the ocean surface.
1 Jan. 2000Princess Weekend
Tom takes Jackie an a Princess Weekend. They are teamed with Susie and her dad Lionel, who is having marital problems. The weekend takes an unexpected turn when Susie runs away, believing it to be the only way to save her family. Lionel realizes that he needs to address the problems in his marriage and be honest with Susie about it.
22 Jan. 2000Black Dolphin
A series of dolphin attacks occur in the waters of Bal Harbor and all fingers seem to point at Flipper. The culprit turns out to be an escaped Navy dolphin trained to protect U.S. property.
19 Feb. 2000The Inquiry
When a routine rescue mission goes awry, Delaney is held responsible. His career hangs in the balance as he is tried for negligence.
Chris finds an old sword whilst diving, and believes it once belonged to the famous pirate Captain Kidd. And where there's a pirate's sword, there's a pirate's treasure. With his friends, Chris goes on a treasure hunt which turns into a comedy of errors.
Holly and Delaney think they've struck it rich when they find an abandoned yacht adrift. The yacht, however, is under a mysterious spell, which affects both Holly and Delaney. Everyone is relieved when the haunted boat finally sinks to its rightful place in the depths of the ocean.
Flipper brings a sick dolphin to the Institute, placing the other dolphins at risk. Alex intends to release the sick dolphin back to the ocean as soon as possible, but her plans change when the dolphin's history is revealed.
3 Jun. 2000The Survivor
Holly and Alex find an Hispanic woman adrift on a life raft. She is suffering from amnesia, and the Immigration Department is keen to deport her as an illegal immigrant. Alex fends them off as Delaney seeks to find out her identity, his only clue being a locket found on the raft.