Jeffrey Wyatt (Barry Bostwick) is the widow father of three triplet girls: Lisa, Jessie, and Megan. As he picks his daughters up from the airport, he neglects to tell them over the summer he has become engaged to Cassie McGuire (Patricia Richardson). Cassie wants to re-design their California beach house with the help of Susan Evers (Hayley Mills), a house designer. Jeffrey initially doesn't like Susan's ideas, but comes around to allowing them due to Cassie.
Lisa, who is dating David, has invited a boy she met in Paris, Hawk, to eat at their house. She doesn't know how to break it to David that she finds Hawk more "un-predictable." She asks Jessie to pretend to Lisa on a date with David, so Lisa can go on a date with Hawk while their father goes on a date with Cassie, Susan, and Nick (Ray Baker), his best friend. At their date, Jessie is bewildered to be at a "Welcome Home Lisa" party with all of their friends. She embarrasses herself during a karaoke dance skit called "The Jackson Three" (a parody of the Jackson Five), singing the Janet Jackson song What Have You Done for Me Lately. The two have a kiss during the date. Hawk, a "bad boy", is not wanting to settle down and be Lisa's boyfriend. He asks Lisa to run away with him, but she doesn't. Later that night, Jeffrey figures out the switch and grounds the girls for three weeks, with David be disappointed in Lisa and Jessie. Lisa unleashes her feelings and tells Jeffrey that she doesn't like the snobbish Cassie.
The next morning, Lisa runs away with Hawk on his motorcycle only to break down at a diner. Jessie and Megan, using David's car, find her. Jeffrey, Susan, and David also find her. Hawk and David begin a fight in the diner, causing the police to be called. Lisa refuses to continue to talk to Hawk and rejoins her family. David begins to like Jessie more than Lisa. Cassie becomes angry that Susan went with Jeffrey to the diner. The girls, who despise Cassie, begin to befriend and like Susan. They set up a date for Susan and Jeffrey by not telling Nick and Cassie to come. Jeffrey expresses his admiration for Susan, who refuses due to the fact that his is engaged. She quits working on the Wyatt's house and continues with Nick's condo. Also, Cassie moves the date to two days away. The girls go to Susan's apartment and discovers Sharon Grand (Hayley Mills), Susan's twin. Sharon agrees to help the girls set up Jeffrey and Susan.
At the wedding day, Sharon and the girls lock Jeffrey and Susan in the garage shed, making Jeffrey miss the wedding. Cassie, jealous, hooks up with Nick and drives away from the girls. Sharon and the girls take down the wall of the shed revealing Jeffrey and Susan about to kiss. They have realized their love for each other after playing the piano and singing to the music box Susan bought and then gave to Jeffrey. Susan moves in with Jeffrey and becomes Lisa, Jessie, and Megan's stepmother.
In The Parent Trap II, Sharon Ferris marries Bill Grand (Tom Skerritt) with their daughters Nicky Ferris (Carrie Kei Heim) and Mary Grand (Bridgette Andersen). It seems that Sharon is still married to Bill. Also, Susan was married to Brian Carey (Alex Harvey). She seems to have divorced him since this movie, even talking about the divorce.
Patricia Richardson and Ray Baker, who played Cassie and Nick, were married in real life but divorced in 1995.
Leanna Creel, who played Lisa Wyatt, played Tori Scott on Saved by the Bell, which is a spin-off of an unsuccessful series Good Morning, Miss Bliss. Hayley Mills played the title-character in the latter.
In The Parent Trap II, Susan mentions her children. In this sequel, she says that the children were from her ex-husband's previous marriage, but she still sees them regularly.