Roberta, an unfulfilled housewife in Fort Lee, New Jersey, is fascinated by messages between lovers Susan and Jim in the personals section of a New York City tabloid, particularly an ad from Jim with the headline “Desperately Seeking Susan”, seeking a rendezvous in Battery Park.
In an Atlantic City hotel, the itinerant Susan reads the ad after a tryst with mobster Meeker. She steals a pair of ornate Egyptian earrings from his coat before departing; the sinister Nolan notices Susan's embellished tuxedo jacket as she leaves. Arriving in New York City, Susan dons one of the earrings, stashing the other in her suitcase in a Port Authority locker. She asks to stay with her friend Crystal, a magician's assistant at the Magic Club, and learns Meeker was killed at the hotel.
Hoping to spot the lovers, Roberta goes to Battery Park and sees Jim reunite with Susan before leaving with his band for Buffalo. Roberta follows Susan to a vintage store, watching her trade in her jacket before losing sight of her, and buys the jacket. Finding Susan's locker key, she posts another “Desperately Seeking Susan” ad to meet with her to return it. Concerned about the ad and Susan's connection to Meeker's death, Jim asks his friend Dez to check on her.
Waiting for Susan at Battery Park and wearing her jacket, Roberta is accosted by Nolan, mistaking her for Susan. Susan spots Roberta, but is arrested for not paying her cab fare. Dez arrives and rescues Roberta, who hits her head and loses her memory. Also mistaking Roberta for Susan, Dez takes her to the Port Authority to collect Susan's suitcase, finding the other earring, and lets her stay at his apartment.
Roberta, believing she must be Susan, retraces Susan's steps with Nolan in pursuit. She arrives at the Magic Club – narrowly missing Susan, who has been released from jail and discovered her suitcase gone – and is hired as Crystal's replacement. After Roberta's disastrous first performance, Nolan attacks her, demanding the earrings, but he escapes as the police arrive. Roberta hits her head again, regaining her memory, but is mistaken for a prostitute and arrested.
Searching for Roberta, her husband Gary finds his way to the vintage store and is put in touch with Susan, who believes Roberta and Dez are connected to Meeker's death and want to frame her. Susan accompanies Gary home, where they get high. Roberta calls from jail, but hangs up when Susan and Gary answer. After calling Dez to bail her out, they find his apartment ransacked by Nolan, and sleep together.
At Gary's house, Susan sees a TV report about Meeker and Nolan having stolen the earrings, once belonging to Nefertiti. She realizes the truth from Roberta's diary, and posts an ad to meet her at the Magic Club. Dez attacks an intruder in his apartment who turns out to be Jim, and confesses to his relationship with “Susan” as Roberta slips away. She reads the ad, as do Jim and Dez; they arrive at the Magic Club, along with Gary, his sister Leslie, and Nolan.
During her act, Roberta recognizes Nolan, who flees backstage. Dez leaves as Roberta tries to explain the events of her disappearance to Gary, finally voicing her unhappiness and ending their marriage. Nolan threatens Susan at gunpoint, but is knocked out by Roberta.
Later, Roberta finds Dez at work in a theater projection booth. She “introduces” herself and they kiss, as Jim and Susan reunite in the theater below. A final newspaper headline reveals that Roberta and Susan returned the earrings.
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