In Brooklyn, New York, a group of masked, hooded figures incapacitate cardiologist Daniel Borenstine with a stun gun and proceed to kidnap his pregnant wife, Jeanie, by placing a chloroform-soaked cloth over her mouth.
Frank and Emma are assigned to investigate the case. Emma discovers that Daniel's office nurse, Rachel Levinson, left the previous month with the intention of moving out of the country. A short time later, Frank discovers an imprint on the doorframe of the Borenstine's townhouse. The shape of the imprint indicates that it was a mezuzah - a small ornament containing text from the Torah (the object is attached to the door jam of many Jewish homes). A technician dusts the place where the mezuzah had been, and discovers a "fingerprint" without the usual swirl pattern.
Emma and Frank search through Rachel Levinson's empty apartment. They uncover a partially painted piece of a broken pot that contains symbols of a bleeding sword and a sacrificial scene. It also becomes clear that a group of interwoven figure-eights is, in actuality, a series of ouroboros. Frank tells Emma that the symbol is quite ancient and not necessarily connected to the Millennium Group. He accesses the FBI's research library for more information on the symbols. It turns out that the iconography is pre-Christian and relates to the First and Second temples. The temples were destroyed and to this day fanatics wish to rebuild a Third temple on the same spot. According to prophecy, once the Temple is rebuilt, the Messiah will appear. Doing so, however, might trigger a war, as a group of mosques occupy the land.
Meanwhile, inside an abandoned Russian bathhouse, Moses Gourevitch and his acolyte, Rachel Levinson, prepare to deliver Jeanie's baby. The pair speak in Hebrew, peppered with an occasional word in English. They lower Rachel into a mineral bath, and she gives birth to a healthy child. Despite Jeanie's pleas, Gourevitch ushers the baby away. Later, Gourevitch instructs Rachel to quiet Jeanie. Rachel injects Jeanie with a sedative. Her unconscious form is later found on the porch of the Borenstine's townhouse.
Jeanie is transported to the hospital, where it is positively determined that Rachel is one of the kidnappers. During the discussion, Daniel reveals that he was approached by someone from the Millennium Group. Frank reviews the hospital's video surveillance footage and realizes the visitor was Peter Watts. When Emma learns of this, she concludes that Watts participated in the kidnapping. Frank warns her not to jump to conclusions. Meanwhile, back at the bathhouse, Gourevitch accuses Rachel of letting Jeanie escape. Rachel denies this is so. Gourevitch then asks to see Rachel's vestment.
Emma and Frank research some of the clues in the case. The unusual fingerprint pattern turns out to be artificial skin developed in Israel to treat burn victims (used by the kidnappers to hide their fingerprints). They also examine photographs of radical groups, and discover Temple symbols (the sword, the sacrifices, the ouroboros) on the shoulder of one member. That man is identified as Moses Gourevitch. A short time later, Frank realizes that Jeanie's maiden name was Cohen, a descendant of the Kohain tribe, a people who were traditional priests. Frank concludes that the radicals will raise the child to become a priest who will serve in the third Temple - and where he will welcome the Messiah. Later, he tells Jeanie and Daniel that the baby was birthed in water to keep him unpolluted (as the earth holds the dead). Jeanie then recalls some of the English words spoken by cult members: "sandwich," "mirror" and "subway."
Rachel decides to go to the FBI. But before she can enter the Bureau's building, she is abducted by cult members and taken to Mount Moriah Park. There, she is found guilty of betraying her cause. Tribunal members stone her to death.
Watts assures Emma that the Millennium Group wants the child found just as much as she does. He tells her that in order to stop the cult, she must think like they do. Watts tells her to read a passage from the Book of Revelation. Upon doing so, Emma encounters a description of images identical to a pattern on the robe that Jeanie was found wearing.
Using the English words Jeanie supplied, and aided by an internal vision, Frank pinpoints Mount Moriah Park. He and two other agents rush to the area, where they discover Rachel's bloodied, lifeless body.
Frank and Emma meet with McClaren and a group of other agents. They conclude that Rachel was executed for bringing Jeanie Borenstine home. Shortly thereafter, Emma reveals that the robe Jeanie was wearing when she was found was manufactured in Brooklyn. She has also discovered that a hot spring runs beneath Brooklyn, one accessed by an old Russian bathhouse that closed in 1948. FBI agents storm the Russian bathhouse. Emma finds the baby in a crib. But before she can take action, Gourevitch pushes a gun to her head. He scoops the child into his arms and orders Emma to walk onto the roof. Gourevitch attempts to make a getaway by helicopter, but he loses his footing and slides down a slanted part of the roof, baby still in hand. At the last moment, Gourevitch makes a decision: he hands Emma the baby. He then falls to his death. The baby is reunited with his parents. Later, Frank tells Emma that it was Watts who sent Jeanie home in the robe knowing that it would later condemn Rachel Levinson to death.