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The actual conspiracy... didn't make much sense (Spoilers Ahoy!)
So the actual plot was killing everyone who knew about the Vice-President's "misadventure" in Guatemala. Fine, in a Comic Book Plot sort of way. But other than the dead reporter, nobody else knew about the VP's involvement. Frank and Co. only found out because Dunning told them. And it seemed as though no one whom the reported had actually talked to was actually talking. Are they seriously trying to say that they didn't interrogate a single one of the targets to see what they actually knew and who they talked to?
Its a comedy dont get to worked up over the framing device.
Of course, it's even worse once you factor in them going after Sarah because Frank was communicating with her. So they were monitoring the two of them, knew they've never met face to face, but assumed Frank told her something? "Wilkes was pulling the strings to make sure no one talked" only explains so much.
Frank explicitly mentions that it wasn't the fact that he talked to Sarah at all, but how he talked to her. They were after her because she could be used to get to Frank.
A lot of people get burned (i.e.: terminated) for a lot less in Real Life. If you've got the slightest idea of who was doing what, you're a security threat.
The whole thing was orchestrated by Dunning to kill the VP. Dunning knew Moses and the rest of them back in their active days (notice they identify the man who collected the package by his looks) and he knew that a simple hit squad could not kill them all and that they would want revenge, either killing the VP themselves or giving him opportunity to do so. His motive is that the VP wants out and he will lose his money, connections and contracts if it comes out that he helped to cover war crimes and used that as leverage to get rich as defense contractor. But if he succeeded everyone who knew about the village and/or could place him there (the pilot) would be dead and he would get away scot-free with most of his connections intact. He probably promised Wilkes to replace the VP as his protegee.
Xanatos Gambit as Dunning would benefit from many different outcomes. If Dunning succeeds in killing everyone connected to Guatemala, cool beans. That's taken care of and no one can connect him and the VP (it is worth noting that no one went after Boggs, probably because by himself he's too nuts to be a threat until Frank got him to join their crew). If they survive, he can continue attempting to take them down with his CIA puppet until they track him down. They're not going to attack him directly because from their perspective he's a puppet of the CIA, not the other way around. If they come after him Dunning can turn them around and point them at the VP to take him out. No loss to Dunning because Stanton wants out anyway and this will take him out and make the survivors of the assassination into internationally wanted killers (or get them all killed, which is also a win). Dunning just didn't expect that Frank would take Stanton alive instead of kill him. If Frank had actually killed Stanton instead of tried to trade him for Sara, Dunning would have won. In fact, if Dunning had never shown up to the factory and instead just sent his goons, no one would have known he was the mastermind behind the whole thing. So the issue is not that the conspiracy made no sense, because it does, but why Dunning risked everything by showing up personally at the exchange to gloat instead of sending his puppets to take care of it. Should have read the Evil Overlord List, Dunning; your plan was going perfectly until you made that mistake!
The Secret Service coverage portrayal for the Vice President was pitiful
It stretched my Willing Suspension of Disbelief - I had to resort to the MST3K Mantra. They didn't have enough agents. They didn't have an agent outside the main door of the ballroom, which would have prevented the door from being locked off. They're rushing the VP out due to a possible gas leak and the fire alarm going off, but there was still no hurry to get out in an orderly fashion. How on earthMoses managed to get his mitts on a presidential limo really pushes it. My workplace was in a restricted zone during a G20. The Secret Service really does think of and cover everything before going in.
They hurried to get the VP out, period, and were knocking people aside to do so. Moses doesn't need a presidential limo, he needs a limo of the same make and a few stickers.
The dropped contact lens shouldn't have deterred the security guards at the elevator
The guards should have just said "That's okay, it can work without your contact lens in. Go ahead and scan it."
At which point they potentially invoke the annoyance and anger of a flag-rank officer who will shitcan their careers. No thank you. They can wait for him to get his contact lens.
I agree. Anyone in the military - especially enlisted like that tactical squad - are trained to fear ranking officers, no matter how unreasonable their requests (read: orders) seem, and the higher the rank, the greater the fear. The Bavarian Fire Drill works a lot better with annoyed eyes in between a pair of four star insignias glaring patiently at you. I still consider the fact that he saluted them afterward, in a sense telling them they were doing their jobs well, makes this scene a very subtle Crowning Moment of Awesome.
Note that the guards are still blocking the general from leaving the elevator, and wait for the scan to be completed. They are doing their jobs, in that nobody is getting in who cannot show proper authorization (even if they don't know its forged). Waiting for the general to find his contact lens before using the scanner is only being polite, and only truly titanic idiots are impolite to two-star generals.
What was the point of the brawl?
If Frank had just taken Sarah and just walked out of there, he wouldn't have gotten shot, and thus wouldn't have had a reason to go to Eagle's Nest. This is why it seems just a bit too contrived. They needed a reason to get him there, so they needed to get him hurt. Why not just have Cooper happen across him? The only reason I can think that this was necessary was to smuggle the Guatemala file out, but first off, there was Sarah's briefcase, and second, once he had the file, Frank said "change of plan" right before entering the office and starting the fight. This means this wasn't the plan all along, so he had another plan to get that file out of there before he went in, and if he was going to try to just talk to Cooper, then he's a lot more gooey and romantic than Victoria thought: gooey to the point of sloppy. Either way, it was a dumb move and seems out of character.
He was going to Bavarian Fire Drill his way into the office, then see what Cooper kn—oh crap, Cooper's here! Time to fight! Alternately, he kinda expected to be able to subdue Cooper quietly. I'm not sure if he looks surprised when he sees Cooper.
He'd gone to New Orleans to see Joe, and encountered Cooper while still in the city. He calls Joe again the next day, and Joe's dead. Knowing about the list, and the fact that there's a CIA hit man in Joe's general area evidently after the people on that list and who has pulled at least Frank's file from the secure archives, it wouldn't be a far leap for him to assume that Cooper is the one who killed Joe. Remember, he doesn't learn that Joe is alive until after the brawl and their escape from Langley. So if he had anticipated Cooper's presence, it might have been a bit of revenge for an old friend and a preemptive strike all in one.
Didn't he steal something of Cooper's while he was there? I haven't seen it recently but I thought the fight was basically half "Let's see what this young punk can do" and half "I need something from his office".
The initial assault
Frank puts some bullets in a pan. They eventually cook off. On hearing gunshots, the bad guys go into full spraying mode and disintegrate his house. So, uh... what was the original plan? If someone shoots, kill off everyone including the guys on our side? Why even give them guns then?
Well, the original plan was to kill Frank in his sleep by lethal injection; we see one of the dudes sneaking in holding a syringe. So, gunshots means that something has gone wrong. Gunshots + no calls on the radio from the inside team means that the gunshots you heard is the inside team getting killed before they even had a chance to know they were being shot at. (Of course that's wrong, Frank had already killed them silently, but I'm talking from the POV of the outside team here). So, since as far as the outside team knows the inside team just walked into an ambush and all died, yeah, you kill everything left in the house. Especially since, from the # of gunshots they're hearing, the outside team probably thinks that Frank isn't alone in there (i.e., that they have walked into a trap).