The episode begins and it would appear that the crew of the Colorado is finally getting some good news, from the looks of it. Basically, Chaplin announces to the crew that in five days a transport ship will be arriving for those who have decided to leave. As a bonus for those who aren't, the government is also sending food and members of the crew’s families. Everyone present seems happy to hear this piece of news. Mostly it's just good PR conclude Chaplin and Sam, but after a gesture of goodwill for the also food-strapped islanders, whose supply ships have been blocked by the perimeter in the form of a belated Thanksgiving, things start to go awry.
After a fun night of breaking bread, listening to music, and playing soccer with the islanders a native woman comes forward to say that one of the crew, Anders, raped her. The islanders seem visibly enraged by this revelation. Tani's father comes after the accused ready to dispense island justice, including 100 cuts with a machete and a branding. Chaplin on his part stops Tani’s father on his tracks and says there's going to be a trial, Navy-style, to decide if the accused is really guilty, as that is the fair thing to do in such a situation. Not everyone is happy with this decision, but have no option but to play along. Chaplin decides there will be a seven person jury with 3 sailors, 3 islanders, and a neutral voter in Sophie.
Sam on his part believes that Anders was the only person rated to handle the nukes. But, it turns out; Chaplin has been tutoring Cortez and believes she's ready, to take over in Anders’s absence. But, Chaplin doesn't know yet that she's the mole who stole the launch key. Shepard is tasked with defending Anders the man who is being accused. She begins her investigation by talking to both the woman and Anders, so she can get both sides of the story and build her case. As she talks to the woman, flashbacks of the alleged rape are shown, from the woman’s perspective. Serrat on his part is the one representing the woman in "court", which is the island church. He stirs up the crowd but Shepard argues that essentially it's a he said-she said scenario and there's no evidence, to prove who is telling the truth.
In the end, a not guilty verdict comes back and the islanders riot as a result. Sophie reports to Chaplin that this is odd since she and two crew members voted guilty and it was the islanders and one crew member who voted not guilty. Chaplin realizes Serrat rigged the jury against himself, as he wanted this riot and the ensuing mayhem. During the riot, as they take cover, Shepard gets Anders to confess that he did in fact do it, which is something she suspected all along. Anders claims it's all Chaplin's fault to which Chaplin does not respond favorably. Turns out, Shepard had admitted to Chaplin that she herself was raped at the academy and was told that there would be no winners if she reported it and therefore had to see her rapist every day until she graduated.
It turns out, it was her rape the scene was flashing back to and she says she knew, as a fellow survivor, that the island girl was telling the truth. Sophie in the meantime, has found the comm site signal being used by the sleeper agent but can't tell Sam where it is so he tries to get it out of the CIA guy who they are still holding captive. He continues to try and gain Sam's trust and turn him against Chaplin comparing him to the delusional Ghaddafi at one point, but Sam says Booth has given him no reason to trust him. So the next time he arrives and Booth shows Sam that he was able to break free from his restraints and could've run at anytime and promises to take him to the comm site, Sam starts to trust him.
They head off for the comm site and arrive late in the day and decide to camp for the night. They trade literal war stories and talk about how memories and images of their wives got them through the worst of the torture. The two seem to be bonding really well and slowly seem to be winning each other’s trust. The next day they head to the comm site. Once they reach the site, Booth types in Sam's question into the laptop; the reply comes that the asset is more important than Sam so Booth tries to kill him. He's surprisingly nimble and effective even in cuffs. The two fight it out trying their best to get the better of each other, but Sam gets the upper hand and kills Booth eventually. He then burns his body, so as to leave no evidence.
Back home in Washington, Kylie tells Christine that Paul has a hero complex and he falls in love with the people he's protecting. Christine leverages this attraction of Paul’s in order to get on the boat going to St. Marie to see Sam. Initially Paul resists this request of Christine’s, but she tells Paul it's so she can tell Sam to his face that she's leaving him, otherwise he won't believe her. Paul apparently seems to be buying this story of hers. In order to make it more convincing, she essentially says the kiss they shared, though wrong, was real and she has to leave her husband as it wouldn’t be right of her to continue as his wife.
Paul in the end buys this and gets her passage on the boat with the stipulation that he has to go with her. Kylie and Christine later overhear Paul talking to Curry who also notes that the two have gotten close and that Paul should see what Christine's reaction is when he drops Kylie's name. Christine prepares to leave and the two women hug and declare their friendship. Shepard on the other hand tells James they can dispense with the niceties and he should pay more attention to Tani since she seems nice and seems to really like him. Tani's own dad was skeptical of her loyalty earlier, telling her that she couldn't have one foot in the water and one foot on the shore. When James protects her in the bar during the riot and then starts fixing the floor the next day she decides to plant both feet in one place and kisses him, basically making her decision about what she really wants.
But, she also hides something in her purse and after he leaves to get more lumber, she takes off with the secret item in her purse. The next morning after the smoke clears and they're leaving, Chaplin tells Anders he's discharging him and arresting him and will be holding him in solitary until he can be taken away. Anders, whose pregnant wife had just sent him a letter, is aghast and instead of being arrested decides to take his chances with surviving on the island until the transport arrives and takes off into the jungle. The episode ends at this point.