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PSO2 NGS Story Guide
The story of PSO2 NGS will likely be complex and long.
This isn't meant to be a substitute for the game, or as a transcript of the entire script/plot, but rather a way to understand, read-up-on, speculate, analyze & get a really good idea of what's going on in the game. It has some game-play hints & will point out ways of approaching story aspects, but it's not really a gameplay guide to get anyone unstuck either.
For online-only games like this, it is important to preserve their plot and characters somewhere that's infinitely stable (unlike youtube or something where the videos get taken away randomly or whatever)
Color key
Green Text: Speculation or opinions
What You Do/The official "Party Line" appears in RED TEXT
Bold Text: Important information
Choice Options: Blue Text
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Nadereh in Halpha’s Energy Plants
You can now find Nadereh in the Dreisen Plant. She’s there with Glen, and says its unusual to meet in here.

What Are You Doing Here?
Why Are You With Glen?

If you ask her the important question What Are You Doing Here? She was told that this plant was like the one in Maquead so she wanted to have a firsthand look. The similarities are uncanny and Ilma said that Lecielans say there are plants like this everywhere.

Even Outside of Halpha?

What does the 2nd one mean? If you ask Everywhere, she doesn’t just mean on our own land, but they’re beyond the sea somewhere too. Glen adds that’s why the West Coast of Aelio was always under attack, and Aelio town was so essential for so long. Nadereh agrees that there could be a plant out in the ocean somewhere. Lecielans believe many are no longer operational but they don’t know for sure. *This harks back to why Garoa was so important to everyone, he was the champion of the most dumped-on area. The plant out in the ocean over the horizon there must have been super active. This was also why he was #1 on Zephetto's hit list to try him against "fake falz" the giant robot to 'test' him to see if he was the Resurgent ARKS--and he died so he wasn't.

Is There A Way To Shut Down DOLLS Production?
How Do We Get Control of The Plants?

If you ask Shut Down DOLLS? She says nothing changed in regards to that, no matter how much the Lecielans tell us our hands are still tied. Glen sadly confirms there no way to stop the production for now. Nadereh says to approach the problem with care, which makes Glen dot at her and be sad/upset. The scene ends.
So now we're finding out that there IS a world beyond the 4 small island/continents even if it doesn't have much breathable air except for where it's domed off over the Creative Spaces and their nebulous 'elsewhere' that Ilma had said during the Creative Spaces speech. It seems likely that it's barren ocean with some hovering Dolls Plants just hanging about though.

Aina in: Zephetto’s Footprints
You can find Aina talking to Crawford on a sunny day on top of the wall at the edge of the city. When you arrive you can choose

What Are You Up To?
What Are You 2 Talking About?

If you say What Are You Up to? To be casual, she’ll say she was talking with him about Zephetto and what he was doing at Halpha, because she wants a hint for dealing with Starless. He explains they’ve been piecing things together from the Lecielans but the problem is that there’s so much data to sift thru it’s 500 years of stuff, and most of it isn’t here at Halpha. Presumably it's up on Leciel's computers.

Has He Really Been Active for That Long?
That’s Hard To Wrap My Mind Around.

If you question with Active That Long? (He said he was, and there’s no reason to not believe him) Crawford confirms that his data has left no doubt, but he wasn’t always a CAST. OH. THIS is news. He ‘made the change’ to extend his longevity for experiments. Aina says he’s so dedicated. Crawford agrees he was so committed.

*SO they are basically confessing and then immediatly disregarding that there is a LITERAL WAY TO BECOME IMMORTAL here. That's like...the most important thing anyone could ever figure out how to do. Unlimited time =unlimited knowledge = unlimited winning. If even 1 person other than Zephetto had been alive through all of this, what sort of a better standing and understanding would everyone have had??? HUGE! But instead she just goes 'wow he sure was dedicated'...uh gee? The peril of the literal universe is at stake and 'golly he was dedicated to stopping the starless from erasing everything everywhere forever' is...a footnote there for ya???

Crawford confirms that he looks like he tried to keep it safe at the start of his experiments, but he didn’t get the results. When he got DOLLS made correctly though, it became like real warfare. A turning point was when he introduced his fake DF. He turned it to survival of the fittest and the defenders who survived saw tremendous spikes in their photon powers. (And presumably their kids' too, that's how we got family lineages like Nadereh's)
Aina glooms saying that’s why we were forced to fight it too…Crawford could never forgive him, but he can understand why he did it. As the leader, he feels the same about the people of Aelio. He’d never take things so far as he did. Crawford says ‘he heard’ that his wish was fulfilled. If it’s true that means we can beat the Starless. At least…so he hopes. He looks to the mountains, and the scene ends.

Crawford never discusses option #3
Safe doesn't work, danger works pretty well, but what if Zephetto TOLD everyone what the plan was? What if he had a power team of the smartest people ever up there, and everyone on the ground working together? Remember, Zephetto's people up there were all unquestioning robo-like-slaves. He wasn't "working together" with everyone, he was just "puppet mastering" alone on his own ideas for 500 years without input from anyone or fresh ideas. This doesn't seem like the best plan. What's smarter than the smartest person alive? A whole team of smart people.

Ah! The macabre question! IS that his original skull??? Who pulled the flesh from it if it is??? Himself? What was that like? Then he embedded it in the blue gel of the empty CAST head? If it’s not his real skull, was he an edgelord that had one casted/molded out of something and then did it to ‘show he was once human’—but he usually keeps it covered up (remember he had a faceplate when you first saw him before he was damaged) because that’s a bit…..icky to do in public.
You can see that he was always all about symbolism, from his name like Jepetto to making Marioness enemies, how the base head has a king-crown border at the top, and he gives himself a halo-like crown apparauts floating behind him as well. So the skull may symbolize something too 'ex-human', or death-avoidance (the skull is 'alive' now), or he is 'like death to foes' because he's a skull.

Very-very interesting that they made him not always a CAST.
It made SENSE for him to be a cast because of the fact that he is indeed amoral. It’s much easier for those to be amoral as they are programmed and not born of a random dice-roll like everyone else…but of course, humans/newmen/duman could probably end up that way as well but they’d likely have to change over time to end up that way (An amoral person).
It’s verrry nice to have a further explanation of “his experiments started off safely” which he, himself had like 1 sentence about, but this is great to elaborate and confirm everything that was summarized above about the experiment that he had told you directly. (Badguys lie, it’s what they do/you can expect it—that’s why characters questioning his everything when he appeared was so refreshing: verify these villains! And that’s exactly what they did)

Crawford in: The Rise of Resurgent ARKS 1
He’s in a meeting to discuss with Ilma, Glen and Nadereh about what to do going forward. You’re there with Aina. Crawford feels that the Leciel research and Starless research efforts are uncoordinated and inefficient so far.  He’s made up a joint research team. Nadereh thinks it’s a good idea, but all teams need a leader, who should it be. Good question, but he’d like to talk to the research team member in Aelio.

You’re Reinstating Her?

If you ask You’re Reinstating Her? He’ll agree that he is indeed doing that, and say he agrees with her, and she’s free now! He needs updates from Manon anyway, and Aina is super happy. She wants to help her with the research she'll be doing (naturally) She says the trio will be back together at last.

Um I’ll Have to Check My Schedule…

Encourage her with Absolutely, but he’ll need you 2 to focus on your own separate duties, your char will have to focus on the Starless and Aina already agreed about the trainees helping. Aina is clearly super disappointed that the trio won’t be back together.

Hearing this, Glen volunteers to lead the team because he delegated to Kanui the combat command of Stia Region. He’ll take care of Manon too because he has too much time on his hands now. Crawford agrees. Glen will need her help too from Aina and any other volunteers. He tells her that she’s got the Arks future on her now. She’s sad but agrees. Glen will help figure out the details once the team is together. Aina is sad and …s but only your character will notice.

It’s unclear whether this is a job with set hours, because if it IS, then everyone could meet up after working the hours no problem. They just wouldn’t be fighting together somewhere. The teleporters do exist in the story plot too, so it’s not like “stia is far and they could never visit”. Also, she’s out and normal now you can literally call her on the video phone any hour of the day.