S01 E01 Phase Six
- The USS Nathan James has spent several months in the arctic under radio silence. The first bit of news they receive from home after this time is that there is currently a global pandemic of a virus that has no cure and has infected 80% of the human population.
- All hands, seal the ship! Rig for imminent nuclear detonation! This is not a drill!
- The Nathan James comes across an Italian cruise ship. When they board it, they discover that the passengers and crew were all infected and died. The ballroom was converted into a makeshift hospital, but only one man is still barely alive and all Dr. Scott can do is give him morphine. The earlier deaths were stored in the ship's freezers, probably both to try and isolate the virus and in the hope that the dead could receive a proper burial later, but as the freezers filled up and more and more people got sick, bodies were left where they fell.
- One sailor trips over a body and loses his oxygen mask. Knowing he's infected and surrounded by the results of the virus, he chooses to kill himself in front of his friend rather than suffer and potentially infect the Nathan James.
S01 E05 El Toro
- El Toro has been using the women, particularly the young girls, of his personal sanctuary as sex slaves.
- El Toro banishes those who he takes a dislking to to an island filled with infected people to die from the virus.
S01 E10 No Place Like Home
- Throughout the first season finale, various members of the Nathan James crew figure out for themselves what Mrs. Granderson's true intentions are:
- Granderson's faction is choosing who gets to survive the Red Flu, under the belief that since the Black Death prolonged the Dark Ages she should ensure that only those she considers to be intellectually acceptable survives the new plague, thus ensuring the United States has an intelligentsia and a loyal police force that can rebuild the country once the plague has run its course.
- The research team working at the pharmaceutical company's building were actually working on a fake treatment that would kill the sick, whom Granderson deemed unworthy.
- The radio broadcasts heard for Olympia in the previous episode were a way to attract the sick to a single location, where those who weren't too far gone already would be given the fake treatment, and the dead would be trucked to a nearby power plant as fuel so that Granderson's faction can have electricity.
- And just in case you thought Mrs. Granderson wasn't that bad, she off-handedly mentions that she had her daughter's girlfriend sent off to a plague zone.
- After Granderson's goons find out that Kara's pregnant, they send her off so that Hamada can harvest the unborn child for stem cells to make a new vaccine.
- Finding out that some of the pirates and mercenaries out there used to be professional soldiers and sailors, who now have no thoughts about killing civilians in order to get the Red Flu cure.
- Sean Ramsey's idea that the Red Flu outbreak is not caused by nature, but by some kind of accident. Turns out that he may be onto it.
- Niels' notion of hiding the virus inside harmless-looking children's toys to "experiment" on people who have not had direct contact with him.
S02 E09 Uneasy Lies the Head
- It can't be denied that it's a Karmic Death and he deserved it, but Niels' expression as he's dying of the red flu is still pretty terrifying.
S02 E12 Cry Havoc
- Sean Ramsey's ultimate fate. He is still alive, but the Achilles sits on the ocean floor and is badly damaged. In addition, he appears to be the only surviving member of the crew. Will he slowly run out of air? Will the ship's reactor meltdown first? Or will he steal a weapon and blow his brains out? One thing is for certain: None of those endings will be pleasant.
S02 E13 A More Perfect Union
- After two seasons of seeing the post-Red Flu world through the eyes of Nathan James, we finally get to hear a bit about what's happening elsewhere in the US: the Northeast is descending into civil war over who gets to occupy the cities while the Southwest is fighting a war to see who gets to control the region's natural resources.
- After a mostly lighthearted episode where the crew gets a hero's welcome in St. Louis and the contagious cure is spread around, the last scene of the season has Dr. Scott getting shot by a holdout from the Immunes.
S03 E02 Rising Sun
- The mercenaries are shown drawing all the blood from a captive before he dies.
S03 E09 Eutopia
- It turns out that the entire plot of this season, beginning with the nightclub attack in Vietnam, was an elaborate plot by Allison Shaw and the US regional leaders to lure Chandler away from the homeland and potentially have him and the crew of the Nathan James killed, just so they could discredit and assassinate Mitchener and seize power for themselves.
S03 E12 Resistance
- It turns out that the regional leaders are using control over food to create a mass force of slave laborers to work in factories and power plants, and to fill gaps in the workforce people are being transported on trains like cattle.
S04 E08 Lazaretto
- Dr. Vellek's plan is finally revealed, and it is horrifying - He plans to deliberately infect the world's new food supply with a drug that chemically lobotomizes people. The trial run for his new drug is deeply unsettling.
- Demetrios, though a Jerkass who had previously described himself to Fletcher as Everything bad that ever happened to you, in the flesh, is completely stripped not only of his aggression, but of his free will. He complies with any command from anyone, and when slapped in the face can only meekly ask the assailant to please not do it anymore. Asshole or not, seeing him reduced to such a hollow shell of a man, coupled with the fact that hes completely aware of whats happened to him and cant even muster the anger he knows he should feel, is horrible.
S05 E05 Warriors
- As Kara and Danny mourn Alisha's death, Kara darkly mentions that Kelsi babysat their son several times. In short, the woman who murdered her best friend had access to her son...