The episode begins and Sam goes for a swim off the island. On the sub, they are alerted to a torpedo in the water. Grace calls to deploy countermeasures. They prepare for impact. The torpedo room is flooded. Captain Chaplin watches as she decides not to surface. He says it's the right call and ends the drill. COB breaks up a fight between sailors arguing about following the captain. They don't have to believe in Chaplin, COB tells them, but they will believe in him. Back on the bridge, they get an Emergency Action Message from DC, alerting them to treason and terrorism charges being filed against Chaplin and Sam Kendal.
Back home, Kendal's wife Christine argues with the bank on the phone, saying her payments have been made on time. She sees the news about Sam and notices a white van sitting outside her house. Back on the island, Redmond's body washes up on shore, for Cortez and Brennan, his former fellow captives, to see. Cortez tries to assure Brennan he had no choice. Kendal plans to interview both of them later. Chaplin and Kendal go back to the captain's quarters and find Chief Anders waiting for him, against protocol. He says he just wants to go home and he's not the only one. After he's escorted out, Kendal tells Chaplin they have a morale problem.
Chaplin suggests they give people the choice to leave. "If we can't trust them to stay, what can we trust them to do?" he says. Brennan tells Kendal what happened with Serrat, leaving out that he suggested Redman be shot and that Cortez bought them some time by being alone with Serrat. The crew reads a posted note from Chaplin giving people the choice to leave. Kendal is upset Chaplin didn't give him a heads up. Tani asks James what he's going to do with the body in her fridge. A SEAL member tells James that Hopper, his wounded team mate, isn't doing well. He is angry to see Grace Shepard at Hopper's bedside. She wants to know what the SEAL team was doing in Pakistan, given that the attempt to blow up the Colorado was made 30 minutes after they picked the SEALs up.
Kendal talks to Cortez, asking her, essentially, to get the women to agree to stay, which might make the men rethink leaving. Grace relays her conversation with James to Chaplin. She's walking with Chaplin and Kendal in the village when shots ring out. Kendal takes off after someone in a navy uniform, who keeps firing at him. He catches up with him. Kendal and Grace talk to Wallace, the shooter, who says he was acting on orders from a "higher authority". He tells them they're all dead. COB tells Grace he's planning on staying so he can paddle her, Chaplin and Kendal to their treason trial. On the bridge, Kendal asks Cahill about communications coming in recently. He plays the message from the Secretary of Defense, in which he gives orders for Chaplin to be killed and the Colorado to be scuttled.
Six crew members got the message. Chaplin doesn't want to punish them for receiving the message. He agrees to take them off the duty roster, but he wants to run a drill on the boat today as scheduled. Sophie sets up a camera to record Kendal talking to his wife, telling her there's something she needs to know. Serrat tells Sophie he expects her to follow through on the scientific research her boyfriend talked Serrat into funding. When Sophie leaves, Serrat turns around and sees James King and another SEAL with guns in his face. They want morphine for Hopper. He agrees. The crew waits to muster and Chaplin walks to the boat unprotected as a show of strength. Anders tells Kendal he thinks the Stay/Go list is a load of crap, because he's the only one who knows how to run the nuclear reactor.
Christine sees news crews setting up outside her house. Kylie Sinclair vents to her dad about their technology being stolen. He confesses he told her boyfriend to take it because the President asked him to. He tells her they have to "sit this one out". King gives Hopper morphine and then asks: "Why did we kill that guy?" "Orders changed," Hopper says. Paul visits Christine, who tells him the Navy cut off Sam's pay and now she's broke. He gives her the $217 he has in his wallet. She doesn't have any family nearby to turn to. He tells her she's going to be under a microscope, but he'll be there for her. Flash bulbs go off outside and she runs outside with a baseball bat.
She sees that someone has spray painted "Traitor" on her garage. She smashes in the window of the white van that's been outside her house then she turns to the media and shouts that the government detained her and she only wants answers and the truth about what happened on the Colorado. Sophie uses the equipment Serrat bought to test for the rare mineral her boyfriend thought was all over the island. Her test vial turns up green. She goes back to Serrat and finds him laughing at the tape Kendal recorded, Sophie asked him to send it. He says he will. She shows him a test tube and tells him if the mineral was there, it would be green.
The one she's holding is red and says they all were. He tells her to keep looking. Back on the sub, they wrap up their drill with improved results. Brennan comes on the bridge and reveals he has a grenade. He tells them to sail to the blockade to turn over the ship. Elsewhere in the ship, Kendal passes out guns, including to COB. Brennan tells Chaplin that everyone thinks they're traitors and he wants to be thought of as a hero. Cortez intercepts Kendal and pleads with him not to kill Brennan, saying he's messed up. Chaplin makes the case to Brennan that they're upholding the constitution. The crew hears their entire conversation played over the loudspeakers. Chaplin asks Brennan just to talk to him. "He's dead because of me," Brennan says.
Just then Kendal, COB and other sailors come on the bridge with guns drawn. Brennan pulls the pin on the grenade and holds it. He demands to talk to Secretary of Defense Bill Curry. They put the call through and put it on speakers. Curry asks what the situation is and Brennan tells him, he asks for orders. Curry says they're too far from the blockade and then tells Brennan to sink the boat. Chaplin reminds Brennan there are 120 people on board. "I'm trying to bring the truth out to light, but I need your help," Chaplin says, calmly reaching for the grenade. Brennan lets him take it. Kylie meets with Admiral Shepard and says she can't help him anymore. He tells her the order she gave him was wiped clean. She reverses course and tells him about the president getting her dad to steal her drive.
There's a sort of GPS built into her system and it would have recorded the Colorado's position on that drive. She thinks it was stolen so that no one would know where the Colorado was before the attack. Shepard has been asked to attend a meeting with Curry, he's not afraid. Two of King's SEAL mates tell him they're leaving and they want to take Hopper with them. He says no and fights them, losing badly 2 on 1. Kylie's dad tells her the stakes are out of her league and she agrees to let it go, but doesn't mean it. Kylie sees Christine's rant on the news and sees a potential ally. Cortez goes to see Chaplin and tells him about Serrat forcing them to choose who would die. "So you let a time bomb fester on my boat?" he asks. She was worried what the crew would think.
King digs a grave for his friend. Chaplin and Kendal watch as people remove their names from the Go list and put them under Stay. Anders notices he's been moved to "Stay". Kendal tells him he's too important to let go. Tani tucks beaten up James into bed. Kendal goes for a swim off the island and sees Sophie waiting for him on shore. She takes him to the hills and tells him they're the power on the island. She then tells him there are things here worth more than he can imagine. The episode ends at this point.