All questions that lead up to this episode have been cleared up in the first few minutes into this episode, and swift turned to destruction just as quickly. We now know Ohara was mass producing Marias so they can act as easily cloned and disposable Pandoras. It makes sense now that it has been revealed, but I'm a bit disappointed in myself for not putting two and two together in this case. Regardless, Ohara's secret plans to prove Aoi Gengo wrong with this has backfired as all the Maria's seem to have speed up Amelia's Nova transformation and were absorbed by the newly formed "unknown type" Nova.
With that, we get reminded of the whole Tower of Babel analogy yet again -- it was introduced back in episode 8. So with the anime insisting on making such an analogy, it feels like the series as whole is trying to say that humans trying to make some kind of progress are making futile efforts when presented with things they don't understand. And a lot of science is experimentation in an attempt to better understand the subject you are experimenting in; if science gave up on things that they currently don't understand, there wouldn't be any kind of progress worth working toward. And that is what Freezing's message is coming to, at least from my interpretation, that being science isn't worth pursuing if there is any type of block -- whether that be lack of knowledge, fear, religion, or any other type of authoritarian push back.
Taking a step past Amelia fully turning into a Nova, there was a lot of Pandora being affected by the new Nova psychologically. These were the females that had high compatibility with their stigmata, one of them being Satellizer. So after Kazaya painstakingly sat and watched Satellizer and Rana get the snot beat out of them by Chiffon, he had to actually do something evolving effort. Using his freezing ability, he was able to hop into Satellizer's mind and try to convince her not to be taken over by this Nova. With the help of Rana, he did accomplish that goal, but this kind of felt like a repeat of what happened not too long ago within this season.
Before the rebelling of E-Pandora, she was dealing with her brother; the main reason Satellizer was under the chains of her brother was because she felt alone, and her brother was the only one she could turn to. Now, I mentioned before during that arc, she should have know Kazuya was there for her during the first season, and this is the THIRD fucking time Satellizer has to be reminded that she has other people she can rely on.
I'm completely fine with a character not remembering some kind of point and being reminded, but Satellizer is a bit amnesic in her forgetfulness since the previous arc was highlighting this exact point. Too much repetition of the same thing can be annoying and Satellizer seems to never learn that she is love or her trust issues might be much more than just her traumatic family history.
The last thing that was introduced before the episode came to it's conclusion was Chiffon and her finally opening her eyes. When Satellizer was being controlled by that Nova, you could see some yellow light peeking through Chiffon's eyelashes. Subsequently after, Chiffon's limiter told Kazuya that Chiffon was different from the other Pandora, and that foreshadowing wasn't dragged for too long when Chiffon revealed something that was called "Anti-Nova Mode".
I'm kind of guessing this is just Nova Mode, and Chiffon wants to stick "anti" onto it, but we will see in the, most likely, last episode -- however those eyes do look similar to the ones one the clones of Maria. We are basically going to end the second season like the first, with a random appearance of a super strong Nova and all the main character Pandora use everything they have to defeat it. I'm assuming that Amelia did get completely taken over by the Nova and is no longer herself, so this will be an interesting final battle. I'm far more interested in how Gengo will deal with Marks' actions and all the after mass of these event, but it's too bad that it will only be twelve episodes again.