Flashback: Rachel's father refuses treatment for his wife's malaria because of his faith.
Rachel harvests Niels' organs for study. Chandler and the special ops team return to the Nathan James. The safe zone isn't a viable option for rehoming the teenagers. The doctors are covering up the cause of Niels' death.
The Immune prisoners are questioned by Slattery.
The President and the officers go over the plans for New Orleans.
Rachel continues her work, but can't get Niels out of her head. She wants to make the cure contagious instead of focusing on aerosolizing the vaccine.
Miller is debriefed on the events leading up to Niels' death. Chandler, Slattery, and Garnett are suspicious that the death wasn't an accident. They launch an investigation, seperating Bertrise, Rios, and Rachel and removing them from the lab.
As the Nathan James reaches New Orleans, Chandler orders the crew to stay on alert for the rogue submarine.
Burk and Wolf discuss Niels death while in the head. Bivas interrupts them, and flirts with Burk about where people have sex on the ship before she gets in the shower.
Ray is being shown around in engineering. The crew discovers that all the cell phones found on the Immune have the same game loaded. It uses Bluetooth to send text messages, which limits it to short range use.
One of the Immune prisoners, Flea, is brought before Chandler and the President. He is easily intimidated.
Rachel is nervous about the investigation, and gets defensive with Slattery. She tries to use her work as an excuse to get out of questioning.
Andrea updates Slattery -- they found an IV bag in the trash with the tubing that Niels ripped out.
Milowsky is looking at Rachel's laptop when she enters the room. He's figured out what she did. He warns her that she didn't cover up the evidence very well. She heads to the lab and injects herself with the new cure, testing the effects on the mice.
Flashback: After her mother's funeral, an aid work comforts young Rachel and encourages her to fight for what she believes in.
Tex visits Rachel, reassuring her that she is the reason the crew is alive.
Miller and O'Connor are given candy and trinkets by the crew, who believe they had a hand in Niels' death.
Rachel reports to Chandler. She tells him about the plan to make the cure contagious, and how she injected herself. Chandler is not distracted from the question of Niels' death. She admits to killing him in order further her research. He admonishes her that she doesn't get to decide what is right, but she holds firm to her belief that she did the right thing.
Chandler reports to the President that Rachel confessed and has been confined to quarters. Michener asks about the opinion of the crew. Chandler is undecided on her fate.
Tex and Green take Flea in towards New Orleans to hack into the Immune communication network. He receives a message indicating the Immune are aware of the Nathan James' presence. As they search for the submarine on sonar and radar, the ships in the harbor start to explode. The Nathan James sets general quarters as the president watches, horrified. A torpedo is lanched at the ship, and they take evasive action. Chandler realizes that the submarine is hiding underneath the civilian ships. The crew manages to evade most of the torpedoes fired, but the last one reacquires and the ship is hit.
The hull isn't breached, and Green requests permission to give aid to civilian victims. The Nathan James can't return to the harbor while the submarine is still there. Sean hails Chandler, and brags about his attack. He sends out a broadcast that's doctored to make it look like the Nathan James attacked the New Orleans flotilla.
The lab is left in disarray after evasive measures. Rachel's cure is proven effective. Chandler is still unhappy with her, and is worried about the fight to come. He hands down his judgement -- she will be allowed to continue her work, but is otherwise confined to her quarters. He tells her that he'll hand her over to authorities to be tried for murder if they can ever find a safe place to land.