Sixteen-year-old Ruby (Leelee Sobieski) and eleven-year-old Rhett (Morgan) lose their parents in a car accident. Their parents' will is not a recent one, but in accordance with its terms the children are placed under the guardianship of family neighbors from some years back, the childless couple Erin (Diane Lane) and Terry (Stellan Skarsgård) Glass, who live in a large glass house in Malibu.
There are early indications that all is not well: the children have to share a room together, they are no longer educated privately, Rhett is allowed to play with games consoles at all times, and Ruby is made uneasy by Terry's sexual hints when they are alone. Ruby comes across unlabeled pharmaceuticals and sees Erin injecting herself, though the couple claim this is for diabetes. Ruby tries without success to get the children's estate and trust fund lawyer to accept her concerns, and a visiting social worker is taken in by the Glass's assurances.
Ruby discovers mail from the children's maternal Uncle Jack (Chris Noth) in the trash, along with a letter from a private school indicating the Glasses unregistered the children and pocketed the $30,000-plus tuition money. Ruby also finds signs that Terry is in debt to loan sharks, and she gradually realizes her new foster parents are after the siblings' $4 million trust fund. Ruby becomes suspicious of her parents' death and discovers evidence of the Glasses' involvement.
After an unsuccessful attempt to run away, the kids are recaptured, the Glasses drug Ruby, and Terry tells Erin they must get rid of Ruby. Overcome by guilt and having lost her medical license due to her drug abuse, Erin commits suicide. Terry locks the kids in the basement and sabotages his car, expecting the kids to make another escape attempt. However, the loan sharks, alerted by Ruby, appear at Terry's house, kill the estate attorney (who has come to confront Terry and revealed his complicity), repossess Terry's Jaguar, and insist on taking a ride. Terry begs them to reconsider, or to at least take another car, but eventually gives in. The car goes over a ledge and crashes, killing the loan sharks, though Terry survives.
Meanwhile, the children are picked up by a friendly cop. The policeman stops at the scene of the accident and, while investigating, Terry knocks him out. After climbing back up the embankment, and armed with a gun, Terry tries to lure Ruby and Rhett towards him. Ruby hits Terry with the police car and kills him instantly. In the end, Ruby and Rhett end up living with their Uncle Jack, who takes them to Chicago, where they visit their parents' grave and embrace each other as the credits roll
