Clain begins to question the Fractale System after meeting Lost Millennium, but it all starts when Phryne jumps into Clain's life. Or, more specifically, when she interrupts Clain while he's currently going through the Fractale System norm of "offering prayers."
It seemed particularly odd that Gail was revealed to be a sculptor in Episode 7 because it didn't seem to be important until it is revealed that Megan, also a sculptress, is his doppel.
Dias claims his reason to help Clain rescue Phryne in Episode 10 is for "love"—to make up a lost thousand years through "the love to willingly sacrifice yourself for others." It kind of makes sense because Phryne made a sacrifice and left Lost Millennium to peacefully negotiate with the temple and in doing so protect the people she cares about, and Dias plans to have Phryne killed so the "key" cannot be created and the Fractale System cannot be restored.
After seeing all 11 episodes you begin to wonder how the show is in any way similar to fractals, from the title. It becomes clearer once you find out what one is: a geometric shape that can be split/duplicated into a reduced copy of itself. It can be explained in a mathematical algorithm, have infinite detail no matter how small, is found in nature, and is useful in technology. Barrot made copies of "the Key" to help preserve the System that operates the services humans use, but whereas fractals normally occur naturally, he made them artificially, and the Lost Millennium saught to break down the System they managed.
Episode 11 reveals The reason why an emotionally abused girl fits as "god" of the fractale system, after all, who else will wish for a world where everyone are hidden from each other? also, the doppels are like the split personality of the original phyrne, as some sort of avatar.
Megan being Gail's doppel, resembling futuristic G.I.R.L. implications.
The Phryne clones. The temple can create as many as they please, and the "useless" clones are destroyed. What's notable is that these clones look like Nessa, but really resemble Phryne from her childhood. Does that mean the temple has been cloning Phryne since she was a child?
Episode 9 reveals that not only Phryne herself and Moeran are Phryne clones, but they're all labeled in six-digit numbers—No. 152589 and No. 141923 respectively). This brings into question on just how many Phryne clones has Barrot created.
Revealing that Barrot is not only Phryne's father-like figure, but he is the one who has raised her to become the "key." Given his questionably intimatetendencies around her, who knows how long Barrot has been "toying" with Phryne and just what he's been doing to his "precious daughter" prior to her escaping the temple.
Episode 10: What adds to how unsettling the former implications were is Phryne mentioning that Barrot has been "defiling" the Phryne clones (including her) countless times and how she constantly refers to Nessa (who resembles Phryne in her childhood) as when she was "beautiful."Does This Remind You of Anything?
What if Phryne's constant stripping without a shred of modesty was the result of being experimented on and "defiled" by Barrot?
So the "happy ending" involves the heroine denying her own self worth and having her memories overwritten by those of a dead crazy girl in order to enslave humanity in a digital illusion, right?