Jenna's life changes dramatically after she meets her OB/GYN, Jim Pomatter, a Connecticut transplant who has moved to the small town to accommodate his wife, who is completing her residency at the local hospital. Jenna and Jim embark on a passionate affair, and eventually Jenna thinks of him as not only her lover, but best friend as well.

Jenna begins to keep a journal, addressing her thoughts to her unborn child. Between these entries and the various pies she creates, the audience witnesses her innermost hopes and dreams, concerns and fears, and slowly growing feelings for the baby she insisted she didn't want.

Reluctant mother Jenna instantly falls in love with the baby girl she names Lulu. When Earl reminds Jenna of her promise earlier not to love the baby more than she does him, she gains the strength to tell him she hasn't loved him in years and will no longer put up with his possessive and abusive ways and wants a divorce. In retaliation he refuses to pay the hospital bills, and she is abruptly discharged.

As Becky and Dawn are helping her prepare to leave the hospital to live with Dawn and her husband until she can formulate a plan for her future, Jenna remembers an envelope Joe had delivered to her when he too was admitted as a patient. In it she finds a handmade card with a sketch of her, a check for $270,450, and a message urging her to start fresh.

As she departs from the hospital, Jenna ends her relationship with Jim and begins her life anew. An epilogue shows Jenna winning a pie contest and as the new owner of the diner where she worked, now called Lulu's Pies, serving brightly coloured pies to her customers and friends. The final shot shows her walking home with toddler Lulu (played by Shelly's actual daughter, Sophie).

The acceptance of Waitress into the 2007 Sundance Film Festival was bittersweet because writer/director Shelly (who also played Dawn in the film) was murdered before learning the news. The film opened to glowing critical reviews summarizing it as a "good-hearted, well-made comedy" brimming with "quality star wattage". Fox Searchlight Pictures acquired the distribution rights for roughly $4 million.