Some things I've been thinking in regards to the vault and how Ozpin acts.
Jaune Arc: What would this school need to...hide?
Given the location of the vault and the talk of the "brotherhood" that Ironwood, Glynda, Qrow and Ozpin have with Pyrrha it seems like it's been around for awhile. It's underneath the tower/Ozpin' s office which begs question of whether the other towers have vaults too. Qrow states that heads of the other two academies and them are the ones really in charge of fighting a secret war. Was this always the case ? The very existence of it seems to suggest it's likely. There has to be other secrets down there too.
Since we know who's involved in the brotherhood the school setting makes sense as the headmasters not only train the next generation they pick important players like Ozpin's interest in Ruby and choosing Pyrrha to be the next Fall Maiden. But I have a few questions that came up during the lead to Ambers' death. Many blamed Jaune but some things keep bugging me about that scene.
If the vault is such a big secret then why isn't there more security? All we see is the heroes get off the elevator and run straight to where Amber is being kept. There's nothing to stand in the way. No system, no robot guards (moot at that point but even so), there aren't even any doors to lock. So did they just put Amber in a life support system with no one to watch her most of the time and just the elevator separating them? "Such arrogance" indeed.
Did Ozpin actually want Jaune to guard the doorway or was he just keeping him busy? No seriously, this is always on my mind when I see it and I've seen the scene several times now. Think about it. He doesn't explain anything to Jaune who had no idea there was anything besides the Grimm and White Fang invasion to worry about. Sure Jaune knows a woman on the speaker is to blame but does he know WHO that is? Later on he sees Cinder and she is referred to as "that woman" I'm not even sure if he knew her from the tournament since even team RWBY missed their fight and only Ruby met Cinder.
Ozpin is rushed and out of options, fine. I get it, while I'm a firm believer in him having plans for Jaune (*1) I don't think he wanted him there. Not only could his presence affect Pyrrha but Ozpin doesn't want to explain the situation for a number of reasons. But Jaune needed some information which could have been provided while they were in the elevator or running. Something to simplify the situation like stating Jaune needs to guard the doorway in case the speaker woman comes and warning him that Pyrrha might be in pain while she powered up. Jaune reacting to her scream was natural and any member of RWBY would have done the same. Yang probably would have demanded answers or want to tear the life support system up to prevent further torment.
But Ozpin suggested Jaune guard the doorway if he wants to help. He does this after Jaune starts getting weirded out and Pyrrha stops to possibly explain. Instead of letting her Ozpin tells her to get to the pod. While Jaune is distracted Ozpin takes the time to get her to choose without her partner interfering. Throughout the time it takes him to start the process right until the moment Amber is shot he seems uncomfortable with the aura transfer. Needing to hear Pyrrha agree to do it and apologizing for what's happening. Ozpin simply can't deal with any of that if Jaune was constantly hovering and he doesn't even care when Jaune leaves guard duty to check on her.
Then there's the simple fact Ozpin knows that anyone coming down to get to Amber would be Cinder or her people. Cinder who already had half of the Fall Maiden' s powers. There's no way Ozpin seriously thought Jaune Arc could be able to stop Cinder. While it's been teased that the blond knight has great potential he's the least trained student at Beacon. Ruby needed Glyndas' help in the first episode just to survive. I can't buy the idea of Ozpin risking Jaune's life even when she's at half strength.
I really think that if Jaune had tried to confront her Ozpin would have told him not to attack just like he did when she was at full power. He even tells Pyrrha that she'd only get in the way if she helped. Now Cinder was at full power when he says this but it highlights how nonsensical it feels to have Ozpin ask Jaune to have guard duty. Plots from the time in the vault might carry over in the future. How Ozpin was apparently captured being one of those stories. Still the entire exchange with Ozpin, Pyrrha and Jaune fascinates me. From a storytelling perspective why does Jaune have to be there?
Well for Pyrrha there's the romantic subplot which gives weight to her sacrifices and will effect Jaune after her death. But what I want to know is whether being in the vault will be important in the future. Will Cinder think he's part of the Brotherhood because he was there? Will Jaune tell his teammates and Ruby about it? Will Jaune try to piece it together?
I know that team RNJR isn't going to Atlas (yet?) but the life support system/aura transfer machine was built there. Given the fact Penny had an aura and Ironwood claimed he could explain her gives me a theory. I think the machine is the same one that created Penny. That she might have been a normal girl that was dying and had her aura transferred into a robot body. The experience changing her into the naive Penny we knew. If they connected the dots it could create distrust with Ozpin.
*1 There's something suspicious about Ozpins' reaction during the entrance exam when the subjects of the Pyrrha/Jaune partnership and Jaunes' transcripts come up. The common theory is that Ozpin is well aware of Jaune Arc being untrained which naturally makes one wonder why he would allow unprepared student into his school.