Agent Trouble is a movie about Amanda Weber (Catherine Deneuve), a museum employee who is on a mission to uncover the truth behind her nephew Victorien's (Tom Novembre) murder. Victorien was against keeping wild animals in zoos and was a witness to a mysterious government project where fifty tourists were killed by poison gas.
Amanda knows that Victorien's death is connected to this project, as the bus they were travelling in was found at the bottom of a lake. Alex (Richard Bohringer), a government assassin with marital problems, is tasked with eliminating anyone who knows about the cover-up of the project. Amanda soon becomes his target, putting her own life in danger.