College professor and Associate Dean of Students Andy Safian (Bill Pullman) and his wife Tracy (Nicole Kidman) are seemingly happily married, except that Tracy has been unable to get pregnant and Andy is currently a suspect in a series of rapes on campus. When Tracy is suddenly rushed into surgery with a ruptured ovarian cyst, the operating surgeon, Doctor Jed Hill (Alec Baldwin) notes that the other ovary is twisted and showing signs of necrosis. With Andy's consent, Jed removes both ovaries but also discovers that Tracy was four weeks pregnant; however, the fetus miscarried due to the trauma, and Tracy is now unable to have any more children. But the real trouble begins when, thanks to the sperm sample he had to provide to Detective Dana Harris (Bebe Neuwirth), Andy is shown to be sterile. The question then arises as to how Tracy got pregnant and by whom.

Malice is based on a story and screenplay written by American screenwriters Aaron Sorkin, Scott Frank, and Jonas McCord.

To increase the size of the lawsuit against Jed. She asked for $30 million but eventually was rewarded $20 million, still a sizable amount of money, double what she would have received just for the removal of a viable ovary.

When Andy tells Tracy that he wants half of the money or he'll tell the police about the 10-year-old neighbor boy who witnessed her Pergonal injections through the window, Tracy tries to talk Jed into killing the boy. Jed refuses, so Tracy shoots him. She then calls Andy to tell him that she will give him the money and arranges to meet him at the northwest corner of Market Square in 15 minutes. After Andy has left the house, she smashes a window in the door to the neighbor's house and lets herself in. She goes up to the boy's room where she sees him at his keyboard. Sneaking up behind him, she wraps a piece of plastic over his face only to find that it is Junior, the CPR dummy. Suddenly Andy enters the room. Tracy rushes at him, knocking them both through the banister to the floor below. Tracy reaches for a broken post with which to kill Andy, but Dana's foot stops her. "I won't mind shooting you," Dana says, pointing her gun at Tracy. The police lead Tracy to a squad car and, while she is sitting there, she sees the boy and his mother return. It is revealed that the boy is, in fact, blind and could not have seen anything. In the final scene, Dana and Andy sit on his front porch. Dana advises Andy to put some ice on his sprained arm, but Andy replies, "I'll have mine in a glass with some scotch...single malt, nothing blended. Blended whiskey is crap. Someone told me that once." They then get up and walk down the street together.