It's been a rough past few days for propulsion engineer Kyle Pratt (JODIE FOSTER). Her husband died from injuries sustained in a fall and she and her 6-year-old daughter Julia (MARLENE LAWSTON) are accompanying his body from Berlin back to New York on a new airliner that she helped design. The first to board, they settle in for an overnight, transatlantic flight.
Exhausted from what's occurred, Kyle falls asleep and then wakes up a few hours later, only to discover Julia missing. She initially thinks her young daughter has just wandered off, but after an impromptu search of the multi-story plane, she begins to panic. The flight attendants, including Stephanie (KATE BEAHAN) and newcomer Fiona (ERIKA CHRISTENSEN), try to comfort and help her, but Kyle insists on speaking to the pilot.
Her rushing the locked cockpit door brings the swift attention of air marshal Gene Carson (PETER SARSGAARD) who eventually arranges a meeting between the distraught mother and the pilot, Captain Rich (SEAN BEAN). Although unorthodox, he orders that all passengers be seated and that the crew search the plane from top to bottom, except for the cargo hold that he deems too dangerous to explore.
Their search, however, comes up empty and there's even more unsettling news. There's no record or evidence of the girl having ever boarded the plane. As the others slowly begin to think she's lost touch with reality for any number of reasons, Kyle does whatever she can and must to figure out what's going on and find the daughter she knows got on the plane with her.