The team suffers a devastating loss and confront staggering challenges. Adapting to the next evolution of The Machine, now completely self-governed and hidden from all, Finch and Reese team with rogue agent Sameen Shaw to save lives and seek justice, but their missions now threaten to tear them apart. Joss Carter and Lionel Fusco finally unravel the criminal police conspiracy "HR" - but at a tragic cost. And former cyber-enemy — and now highly tuned confederate of The Machine — Root becomes an unpredictable ally when the team learns a second surveillance apparatus to rival The Machine is on the verge of activation.

A supercomputer developed by reclusive billionaire and software genius Harold Finch analyzes data patterns in surveillance for the U.S. government to identify impending acts of terrorism. But the computer, known only as "The Machine", can also identify ordinary people who are about to be involved in violent crimes. Can those crimes be stopped before they take place? Secretly tapping into The Machine, Finch and ex-CIA agent John Reese use vigilante tactics and state-of-the-art technology to identify the soon-to-be victims and prevent the crimes from occuring. Meanwhile, two NYPD detectives Joss Carter and Lionel Fusco are drawn into the cases and the mystery surrounding the two covert crime fighters.