Honestly, I think it kind of comes down to this:
Being Whole may just translate to being Happy. Most of these girls are "happy" with how things are, even if it's not perfect. They are happy with their script that they were given. Happy to play the girl they are scripted to play.
When they truly go off script is when they become aware. When things happen that change who they are and what they want, or when they are not "happy here", they seem to become aware. Sana, for example, is wanting to be
Happy, now:
Which seems to have made it so that she can acknowledge the reality of the world. She's not the same character she was scripted to be. She just didn't care about the weird things going on, until Sensei mentioned it.
- Ayane had been happy until she got knocked up, and then lost the baby, which she still remembers. She wanted to be a mother, and that's what made her happy, what kept her going, but this world wouldn't allow that. She's had to go off script to be happy ever since.
- Makoto has had to change again and again since Bluejay to be Happy. Bluejay broke her, then she was reset, but the memories of Bluejay forced her to try to change, then her father's death nearly broke her, but Ami helped her (Ami's the caretaker and cared for both Ayane and Makoto before they became aware), which allowed Makoto to instead focus on what makes her Happy. This is when the Unbluejay happens, she tricks Sensei into signing marriage papers, and then she's shown to have become aware of things. Her trying to be Happy, instead of simply being "happy here", may have been why.
- Yumi was forced to re-evaluate what makes her Happy after Nodoka forced her to face herself, Chika, and what her future might look like (Yuki). This led to her trying to be Happy, by letting Yuki back in, being nice to Noriko and Futaba, etc.
- Tsuneyo is a little different, but assuming that what happened to Molly forced her to re-evaluate what makes her Happy, then Sensei taking her on that date also changed what she thinks will make her Happy (Sensei), then this may explain why she's become aware.
Nodoka seems to be trying to liberate everyone, presumably like her mother tried to, in the past, from the script. From the game. She's doing this by more or less:
However, trying to break the mold seems to have crippled Nodoka's mother mentally, and may do the same to Nodoka. Kyoko didn't seem to have a Sensei to help like Nodoka might, though:
For those unaware, Nodoka's mother isn't able to take care of herself:
And we presumably know why, now. She fought the world, alone, and...
lost.
Although, like Nao has pointed out:
I'm not sure if Nodoka's attempt at liberation is because she's actually smart enough to escape her script, or if it's simply
how she was scripted.
Her noticing the stain, and her notes, may simply be what's supposed to happen, but if so, then who's to say that becoming aware, or getting to the roof during a reset, isn't part of the script.
We know it
technically is, but if Sel is going that route, then this really can only end rather depressingly.
Edit: Also Maya and Sensei may have become aware because without eachother they weren't "happy here".