Three months earlier, Sean loses control of his F-22 jet and crashes in the Sahara. In present day, Sean is being interrogated about what happened next in a room full of government officials, including Wes and Frommer. Sean concludes that whatever the fulgurite rock is, it wants to destroy them. Wes states they know now that the being chooses to only communicate through children. Meanwhile, the president’s wife and her daughter Cassandra are en route to the White House. During the car ride, Cassandra asks her mother to borrow her phone to play a game.
Secretary Frommer and Sean are left alone together, with Frommer questioning him. The two get into a heated conversation and Sean is given an ultimatum: do as he’s ordered and let them know what they’re up against at the black site, or go to jail. At the black site, Wes and the president examine the fulgurite. The president makes up his mind and comes to a decision to protect the rock. At the Bennigan house, Sean returns home to an excited Henry and a surprised, but welcoming Claire.
Getting back into his car, the president discovers his daughter’s favorite doll under the seat, leading him and Wes to converse about their families. At the Lawrence house, Lena and Minx are sitting in the backyard and making contact with Drill. Arriving home to his family, Wes interrupts their conversation and Minx reminds Lena that Drill doesn’t want Wes to know about the game; it has to be their secret. Claire and Sean have a brief but awkward encounter. Later, Wes calls Claire to check in on her and the two discuss Sean’s return.
At the White House, Cassandra is getting ready for bed when her mother asks her about the whereabouts of her phone. Cassandra nonchalantly brushes it off and once left alone, she sneaks into her bedroom closet and makes contact with her new friend, Drill. The next morning, Henry finds Sean in the kitchen; he made breakfast. Sean breaks the news that he is leaving on a new mission and Henry doesn’t take the news lightly. As Sean takes off, Claire follows after him, concerned for Henry. Sean explains the Pentagon gave him two choices: be their guinea pig or go to prison. He chose the only option that protects their son.
At the black site government facility, Dr. Tully and Sean converse about the fulgurite rock. Sean doesn’t hold back his feelings about Drill and tries to recruit her into helping him stop Drill. Angry, Claire ambushes Wes at his house for not telling her about Sean’s predicament. Wes defends himself, saying he’s doing it to protect their children. Later, Claire meets with Jessup, who gives her an FBI tactical vest. When he inquires about her need for a vest to watch Henry, she reasons it’s for their safety. Jessup doesn’t buy it and drives away, sneaking back around in time to see her altering the vest.
Lena continues to talk with Drill and tells him that she will help him with whatever he wants as long as he leaves Minx alone. She discovers Drill is with a new, important friend. Sean tells Dr. Tully about his first vision, a vision of things to come, before the crash. On the phone with Wes, Lena tells him what Minx told her and the two try to figure out who Drill’s special new friend is. Wes realizes the President’s daughter’s doll has something to do with it and races to the White House. He frantically searches Cassandra’s room and explains there may be a tracking device that could lead Drill to the rock. Hearing a buzzing coming from the closet, he finds the missing phone with a tracking app.
Armed with the vest, Claire attempts to see Sean at the black site and gets clearance. Wes calls her to warn her about Drill’s knowledge of the rock’s location, but she sends him to voicemail. Meanwhile, Jessup reports to his superior about Claire, who knows where she is headed based on Jessup’s report. Claire reaches Sean – she has what he requested her to bring hidden in her vest. Sean informs Claire that Dr. Tully is in on it with them. The three work in attempt to destroy the rock but are interrupted by the Air Force. Dr. Tully is shot right before Wes arrives and the lights go out. Drill enters the rock.
As the blue light brightens, Wes orders the Air Force to stand down. As Wes tells them to evacuate, Claire pleads that they can get rid of Drill for good and he pauses. Sean tells Wes to take Claire and she realizes he’s going to stop Drill on his own – a feat that could end up killing him. Wes takes a frantic Claire into the room above and watch as Sean destroys the rock. After the explosion, Claire and Wes assess the rubble and find Sean… alive. They believe they have destroyed Drill. Meanwhile, the Cavalry is coming, so Wes tells Claire and Sean to run while he fixes the mess.
Parked outside of the Bennigan house, Jessup gets an order to pick up Henry and get him into the FBI’s custody. At the Lawrence house, Lena wakes up to find Minx at her bedside. She has a message from Drill, who is very much alive and has returned to take Lena up on her offer.