Jenna (Keri Russell), a waitress living in the American South (though the movie was actually shot in and around Canyon Country, California), is trapped in an unhappy marriage to a jealous, controlling, and abusive man named Earl (Jeremy Sisto). She works in Joe's Pie Diner, where her job includes creating the unique pies of her life, such as the "I Don't Want Earl's Baby" pie (aka Bad Baby pie) she invents after her unwanted pregnancy is confirmed. Jenna longs to run away from her dismal situation, and is hiding money to do so. Her only friends are Becky (Cheryl Hines) and Dawn (Adrienne Shelly), her fellow waitresses, and Joe (Andy Griffith), the curmudgeonly diner owner who encourages her to escape from her bad marriage and begin a new life elsewhere.
Jenna's life changes dramatically after she meets her OB/GYN, Jim Pomatter (Nathan Fillion), 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 colored pies to her customers and friends. The final shot shows her walking home with toddler Lulu (played by Shelly's actual daughter, Sophie).