Baldwin, a Chicago architect, loses his wife Maggie to cancer. He and his young son Jonah start new lives in Seattle, but Sam still grieves.
18 months later, on Christmas Eve 1992, Jonah—who wants his father to find a new wife—calls into a talk radio show. Jonah persuades Sam to go on the air to talk about how much he misses Maggie. Hundreds of women from around the country hear the program, and touched by the story, write to Sam.
One of the listeners is Annie Reed, a Baltimore Sun reporter. She is engaged to Walter but feels there is something missing from their relationship. After watching the film An Affair to Remember, Annie impulsively writes a letter suggesting that Sam meet her on top of the Empire State Building on Valentine's Day. She does not intend to mail it, but her friend and editor Becky does it for her and agrees to send Annie to Seattle to "look into doing a story on those radio shows."
While dropping Victoria off at the airport for a flight, Sam sees Annie exiting from her plane and is taken by her, although he has no idea who she is. Annie watches Sam and Jonah playing on the beach together but mistakes Sam's sister Suzy for his girlfriend. He recognizes her from the airport and says "Hello", but Annie can only respond with another "hello" before fleeing. She decides she is being foolish and goes to New York to meet Walter for Valentine's Day.
With Jessica's help, Jonah flies to New York without his father's permission, and goes to the Empire State Building in search of Annie. Jonah goes to observation deck and asks every unattached woman if she is Annie. Sam, distraught, follows Jonah and finds him on the observation deck. Meanwhile, Annie has seen the skyscraper from the Rainbow Room where she is dining with Walter and confesses her doubts to him. They amicably end their engagement. She rushes to the Empire State Building but the observation deck has closed. Annie convinces the guard to allow her to go to observation deck (An Affair to Remember is the guard's wife's favourite movie) and arrives just moments after the doors to the down elevator close with Sam and Jonah inside.
In spite of the observation deck being deserted, Annie convinces the elevator operator to let her take a quick look around. She discovers a backpack that Jonah has left behind. As she pulls out Jonah's teddy bear from the backpack, Sam and Jonah emerge from the elevator, and the three meet for the first time. Annie asks Jonah if the teddy bear is his, and he says it is. "Are you Annie?" Jonah asks. She nods yes, and Jonah smiles. "You're Annie," says a stunned Sam. The elevator operator clears his throat. Sam indicates they should go, momentarily making it unclear what his intentions are, until he says "Shall we?", offers his hand to Annie, and the three go down the elevator together.