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1* Is there some valid reason they're not heading to and checking out isolated but populated islands the virus may not have gotten to yet, but still may have power, industry and laboratory facilities? There must be thousands of potential islands in the Caribbean they are passing.
2** Now that they know the Russians are chasing them, they probably don't want to put any civilians at risk. The Russian admiral nuked a French naval base just to keep the ''Nathan James'' from docking there. He's probably not going to be any nicer to some random island in the West Indies.
3* Chandler tells the Russians that he has control of 'all the food on the island' when they have him blockaded in Guantanamo Bay. No, Captain. You have all the food in ''one warehouse'' on a very big island. A Russian admiral probably knows of one or more Cuban bases where he could resupply without any pesky Americans in his way.
4** Though in order to get to any of those warehouses, the Russians probably would have had to move away from the bay, which would allow the americans to leave.
5* Tophet's presence in the engineering space near the halon controls makes no sense at all. A civilian would not have that much access aboard ship. He's been aboard the ship for ''how long'' and doesn't know how to control the temperature of his cabin? His lie to the watch stander should have immediately sent him to the brig for some hard questioning. And there is ''absolutely no way'' a trained scientist would not know what halon is, or what it does--let alone mistake it for air conditioning controls!
6** He could have been playing dumb about the halon controls, but it ''is'' true that his behavior was suspicious and he still should've been taken to the captain or the XO.
7* Where was the helicopter the whole time the ship was experiencing a water shortage? It could have been used to scout ahead to the island where water was ultimately found and could have brought back water to the ship to help alleviate the shortage (maybe not ''all'' the water it needed, but enough to keep the crew functioning) and in a matter of hours rather than days. A couple of ferry-flights with an improvised water tank could have done the job, and avgas is available as close as the nearest intact airstrip should that be a concern (lots of these in Central America and the Caribbean).
8** SH-60 Seahawks run on JP-8 jet fuel, not avgas. It's more expensive and not available at airports that don't service jets on a regular basis. There are airports in the Carribean that could have some, but the ship would have to dock there or at least anchor nearby, as the Seahawk could never carry enough to cover more than one or two flights. Then there's the question of whether any given airport still has fuel (assuming it wasn't already taken, leaked out of an unmaintained system, burned, etc.), plus the risk involved in going ashore. They already have enough problems so that putzing around the Gulf looking for jet fuel is not going to be a priority, so Chandler is restricting the helo and its fuel supply to absolutely mission-critical flights only.
9* Jamaican survivor Bertrice is immune, so now we know some people have a natural immunity to the virus, allowing a vaccine to be developed. But why didn't anyone test Tex, or the jihadis at Guantanamo--all of whom were exposed and all of whom survived the virus?
10** It's likely that he may have been tested and found to not be immune and simply never was exposed due to the relative remoteness of Gitmo from more well-travelled areas of Cuba. The jihadis were also not exactly amenable to being tested.
11*** That doesn't explain why everyone else on the base died.
12*** Camp Delta (the detention facility) is one small and isolated section of the much larger Guantanamo Bay Naval Station. Gitmo was exposed to the virus, probably brought by a servicemember or contractor who didn't know they were sick. Tex explicitly says that his team and their prisoners were isolated with their own food, water, and power from the rest of the base, and even the rest of the already-secured detention facility, because of the prisoners' high-value nature. They avoided going anywhere near the affected areas once it became clear what was happening.
13*** Given later estimates that 1-5% of the population is naturally immune, there ''should'' have been a few hundred survivors at the base given that there are usually about 9500 military personnel (not counting contractors, etc.) stationed there.
14* Ruskov knows that he has an armed party aboard his ship freeing Chandler, Tex, and Tophet's family. He's getting no response from the engine room. If the party is topside his watch standers will have spotted them, so they're still somewhere inside the ship. Why not just order all hatches sealed fore-and-aft? The escapees will be contained, and the ''Vrenya'' subjected to a compartment-by-compartment search until they are found.
15** He had armed men positioned at all hatches leading out so that the American boarding party would be immediately slaughtered. He was fed up with dealing with Chandler at this point and wanted to end things as quickly as possible.
16* [[PoorCommunicationKills You know, the entire conflict between the Russians and the Nathan James could have been avoided if they were just forthright with what their situation was.]] They are both seeking a cure and possess information that is useful to the other, so if the Russians hadn't been so aggressive, the Nathan James probably would have just given the Russians what they wanted and received the Russian research in return.
17** Then again, Ruskov isn't exactly in his right mind, as subsequent events would show.
18* If Chandler is the highest-ranking member of the US military (or at least the US Navy) still alive, then the best place for him would be back at Norfolk, coordinating the entire relief and reconstruction effort. If he is not, then why didn't he seek out a higher command authority once he reached Norfolk?
19** Addressed in the Season 2 finale. Michener orders Chandler to settle in St. Louis to become the new Chief of Naval Operations because they now need to oversee the administrative side of rebuilding the United States of America.
20* What on earth are they going to do with Niels Sorenson? He's a walking Typhoid Mary, so he either has to be permanently quarantined, or made very permanently dead. In addition, are they going to put him on trial? He has committed crimes against humanity by purposely exposing people to a highly dangerous disease, both through his own generation of the plague, and also by attempting to lure people to infected children's toys. That alone could be construed to carry the death penalty, especially if military law is deemed to apply.
21** As of "Uneasy Lies The Head" it seems Rachel Scott took matters into her own hands.
22* In "Uneasy Lies the Head", Niels and Rachel both agree that the only way Rachel can essentially make the cure contagious is to kill Niels and harvest his lungs/DNA/whatever. In the next episode "Friendly Fire", she claims that she could have done so ''without'' killing Niels. Obviously the writers did this to make her murder of Niels as controversial as possible (wasted effort in this troper's opinion), but it's still a rather glaring script error.
23* Some officials in the USA have pretty short memories, or didn't pay much attention in history class: rationing as an accepted economic strategy to deal with unforeseen imbalances in production vs. consumption was used during World War II and the Korean War, and to a lesser extent, attempted in the 1970s. Why have the writers not had Michener using this very line of argument?
24** Those examples were isolated incidents, and most of the people alive for them probably aren't alive after the plague. America as a whole doesn't have a culture of rationing, its not something most Americans ever dealt with.
25* What happened to Alaska? As of Season 3, with the [[spoiler:Senators' plot to divide the nation up into their own private countries]], Alaska seems to have ceased to exist as a part of the United States. It's implied, if not outright stated, that Hawaii is still under American control, so what about Alaska?
26* Okay, so the regional leaders are grabbing political and economic power for themselves and are forcing people into power plants and factories. But who can they sell the surplus to? If they're purposely forcing down the average person's standard of living to near starvation levels, then the average citizens won't be able to ''afford'' the stuff that's being put back into production. The world's population has been drastically reduced and every country is still recovering - so who's gonna buy what they're making? The whole exercise seems to be shortsightedly foolish in the extreme motivated by greed.
27** A behind-the-scenes video explains that the regional leaders aren't producing anything to sell. Instead, they're trading resources and producing just enough for the sole purpose of maintaining absolute personal power within their territories.
28** They're also paying their workers with food. They probably weren't making consumer goods, but having them work in power plants, farms, or producing equipment for the military.
29* Is it ever explained how the plague ravaged all the world's naval forces so effectively? The ''Nathan James'' is only gone for a few months so there have to be dozens of ships and submarines that left before becoming infected ''and'' after it was known that allowing anyone new aboard would be dangerous.
30** Crews require food and ships require fuel and replacement parts. Even if they knew about the virus and decided to stay at sea as a safety measure, there would come a time when the commanders would have no choice but go ashore or barter with another ship and risk exposure.
31*** In Season 3, Captain Meylan is said to have taken his ship to a small seaside town on the west coast and established and maintained a plague-free safe zone that saved thousands of lives. Under the circumstances, it's by far the best he could have done.
32* How in the hell did one of the four ''Iowa''-class battleships disappear without anyone noticing? How did the Colombians manage to hide it while preparing for their war of conquest? And where on God’s green earth did they come into a supply of 16-inch ammunition, again without anybody noticing that it was missing? The ''Iowa''s are indeed extremely potent warships that would still be a force to be reckoned with today if reactivated, but you can’t exactly grab the keys and drive off with one. All four are museum ships now. Granted, they are supposed to be maintained in such condition that they can be reactivated in time of war, but their magazines are empty and the shells their big guns fire are not the kind of thing that just any old factory can turn out. Operating a battleship is a tremendous logistical undertaking, with the US Navy being the only fleet in the world with the capacity to do so (China and Russia maybe could IRL, if they had any battleships, which they haven’t since 1895 and 1946, respectively). So one of our battleships and tons of stuff that goes boom just walked off and nobody found it out of the ordinary. Somebody (plural) seriously needs to be tied up and shot for letting that happen, plague or no plague.

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