A man on an international flight injects himself with an insulin pen, which releases a biological agent that quickly kills everyone aboard by causing their flesh to crystallize. The airplane's autopilot system lands the plane at Boston's Logan Airport, where various federal agencies create a task force to investigate what occurred during the flight. F.B.I. Special Agent Olivia Dunham (Torv) and her partner, Agent Scott (Mark Valley), are together in bed at a motel, where Scott says that he loves her. Dunham receives a call from her boss Charlie Francis (Kirk Acevedo), who tells her to head to the airport. Dunham is added to the interagency task force headed by Phillip Broyles (Lance Reddick).
Following a tip, Dunham and Scott are sent to a storage facility where they uncover a biochemical laboratory, which explodes when detonated by a suspect they are chasing. Scott is affected by the chemicals released in the explosion, and is placed into an artificial coma to slow the progression of the chemical reaction. While investigating a possible cure to Scott's condition, Dunham blackmails Peter Bishop (Jackson) to gain access to his father Dr. Walter Bishop (Noble), whose top-secret work at Harvard in "fringe science" resulted in him being sent to a mental institution. Dunham manages to release Walter from the institution; however, he becomes enraged when he discovers his laboratory in Harvard has been shut down. Broyles reopens the laboratory, where Dunham transfers Scott's body. To identify the man from the storage facility, Walter synchronizes Dunham's brainwaves with the comatose Scott's so that she can read his mind. Walter claims that syncing brainwaves, and even reanimating the dead, can be accomplished up to six hours after death. With the help of Dunham's assistant, federal agent Astrid Farnsworth (Jasika Nicole), the experiment succeeds. Dunham identifies the man in Scott's memory, Richard Steig, as a passenger on the plane. The team learns Steig's twin brother was an employee of Massive Dynamic, a company founded by William Bell, Walter's old lab partner.
Dunham goes to Massive Dynamic headquarters and meets with executive director Nina Sharp (Blair Brown), who agrees to give her all the information on Steig. The suspect is arrested and initially refuses to provide a list of the ingredients present in the toxin, but Peter's threat of exposing him to the chemicals causes him to reveal the ingredients. The information provides a cure for Scott. The suspect reveals that he did not sell his chemicals, but was forced into what he did by someone from Dunham's office. The suspect leads Dunham to a buried tape recording of his phone conversations about the chemicals and the attack, where Dunham realizes that Scott was involved with the attack from the beginning. While she races back to the hospital, Scott awakens and kills the suspect. He is chased by Dunham, but crashes his car and is mortally wounded. Before he dies, Scott asks Dunham why Broyles would send her to investigate the storage units in the first place. Dunham convinces the Bishops to stay and help her with her new work, which Broyles describes as a task force to investigate events related to "the pattern". Elsewhere, Scott's dead body is brought to a high-tech lab, where Sharp orders that Scott be interrogated, since he has only been dead for five hours.
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