Question: When Ilsa presents Ethan with his supposed 3 options, she says she's proof the Syndicate exists, but I'm not sure how exactly. She also says the CIA wouldn't believe them right afterwards. They all assume at this point the disc is a ledger though, so why wouldn't that definitively prove the Syndicate is real? I know of course that since it's encrypted they can't open it, but Ilsa doesn't know that! I don't see how she could come to the conclusion that the CIA won't believe them.
Question: How long has it been since the last movie? It is said in the fake mission briefing in the beginning that Ethan has been tracking the Syndicate for "the past year", a mission he received at the end of the last movie. Yet I've also heard that the movies are set in the years they come out (2011, 2015, etc) In either case I find it hard to believe that the IMF has not received a new secretary yet if it has been well over a year since the last one died. At the end of Ghost Protocol the IMF is already up and running again. Why haven't they appointed a new head? And who is giving orders/missions in the absence of one? Who gave Hunt the mission to investigate the Syndicate at the end of GP for example?
Question: How did Ethan figure out Atlee's true intentions? He only just learned his name a bit earlier and now he's impersonating him and know exactly how to play him, that he's trying to hide the Syndicate, that he created it, that the PM knows it too. How did he learn all this?
Question: What exactly were Atlee's intentions with Ilsa? Why did he originally send her to infiltrate the Syndicate and why did he send her back later in the movie? If all he wants to do is keep the Syndicate hidden, what does he hope to accomplish with Ilsa as his woman on the inside? Does he actually know what is on the flashdrive she brings him, or does he also think it's a ledger? It makes sense for him to want to delete it in both cases, so I'm confused trying to figure out which it is. Either way, does Atlee send her back to get killed? Hunt later says he wanted to "frame" her, but I don't understand how.
Question: Why is it not possible to breach the security at the storage facility and use the robotic arm to swap the cards? It is an option never discussed.