A terrorist cell based in China called Dark Cloud has devised a plan to release a deadly poison on entire nations using rocket technology. In true six degrees-of-separation style, Agent Sydney Bristow's friend from graduate school, Keiko Terajima, happens to be the daughter of a prominent Japanese physicist, and Dark Cloud needs his top-secret knowledge to carry out its devious plan. What's more, Keiko's married to Franklin, the son of an old colleague Jack Bristow killed years ago to protect Sydney. When APO learns that Franklin is part of an elite group of agents who marry women to gain access to information, Sydney begins to question his true intentions with Keiko.

Tracing the connections leads deeper and deeper into the terrorists' plot — with Keiko's father and husband at the centre. Suddenly, Sydney finds herself on a mission not only to prevent the poisonous rain from devastating a country, but to save her loved ones as well.