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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.
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
It starts out with a fine day on a tropical looking place /beach with Aina and her pal Mannon.
A Meteorn pod crashes down near by, and they go to investigate because these pods often have good people in them, called Meteorn. Aina is an older-teen looking sort with blue hair and red eyes. She's a middle-tan color. Mannon looks older than she is, maybe 18 or 19 or so, and is a lighter sandy tan, with darker wood-colored long, straight hair. Aina is energetic and eager, while Mannon seems calm and reserved.
When they reach the pod, they get Your Character out of it. They're happy to see another Meteorn person because those generally end up helping the town. You're then invited to go to the townm called Ailio Town and meet everyone. The trip to town is used to explain several things about how the game works like photon dashing, photon double jumping, photon gliding & Restasign.

Photon Moving-
Planet Halpha (whatever it may be) clearly is super-duper photon-rich somehow and everyone there clearly has a huge affinity for the stuff because they can concentrate it into their feet to produce double jumps/high-jumps, propelled-super-fast running and also indefinite gliding through the air. Everyone takes it for granted that your character can do this too, despite it being technically 'some type of alien'. Interestingly, even though these people are different (been there for probably 10 generations) you CAN do the photon movements they can, right out of the gate. Sooooo that shows it's the PLANET that's allowing for it, not the people-type. (Remember, not all ARKS people could use photons much at all, remember Ulc? The whole point of her was that she couldn't do it and was an illustration for the ARKS-species of people. Would Ulc be able to do anything here? Your character in PSO2 was always "said to be very photon-affinity" so it isn't out of left-field that it could do all the things here.)

They don't seem to use dimate/trimate/moon atomizers here. There are things called Reversasign & Restasign that look like glowing stems that grow up out of the ground randomly. You can pick them up like any object and upon 'using' the stem it does the same as what it's named after. They have no explanation for how/why the planet produces these.

On the way to town:
Dolls appear and you have to fight them. Defeating a few will bring out a ton more so a cut-scene has to happen where Aina's dad Garou has to come in and bash them all with his giant rare axe weapon to help out. Her dad is the same color she is, with blue hair, no shirt and a somewhat tropical look. His hair has a white stripe through the front of it. The father, after beating the Dolls encourages you to go to town too, to meet him and see the town.
After using Photon Glide you can see their sea-side village. This shows you the unusual mix of high tech stuff like cube shaped cement buildings with glow-lines in them mixed with low-tech where they've built like...tiki-roofs over various things and log-buildings. There's some small-plot farming going on and people's clothes are a mix of the metal/plastic stuff and clearly things they've made out of natural cloth and materials.

It turns out Garou is the mayor or leader of the town.
He lives in a huge house toward the back of town with colored ribbons all around it. Inside is mostly an office of some sort with chairs and screens set up at tables. He invites you to stay at town and learn from the residents. This lets you loose in the town to talk to the people who have various simple requests like hitting targets to help train or getting rid of ALTERS like Oodans and such who tear up the crop fields.

After spending the day doing that, Garou wants to throw a welcome BBQ party for you at sunset, like they do with all the Meteorn they find. The people of the town do like to party, so it works out well. You also learn from Garou that Mannon is also a Meteorn, but she remembered a few things. (Unhelpfully, no one mentions what) Aina and her father are obviously pretty close despite him being busy. He's always trying to train her to get better at being a Dolls-fighter/hunter/whatever they're going to call it here. She wants to make him proud / live up to expectations but she's a bit wishy-washy, though she tries hard and is an earnest person.

However, a Dolls attack happens right in the middle of the BBQ party, and you have to fight them off with Aina and Mannon. All doesn't go well though, because defeating the small-fry brings out a gigantic space ship. Like, skyscraper sized or so, that hovers in the air somewhat out to sea. This thing works up a huge blast and ruins the general area. Garou tells everyone to literally head for the hills, he's going to try to do something about it with his axe. Aina doesn't want to go, but Mannon persuades her and everybody gets out of dodge.

Her dad assumes and yells to everyone that this must be "Dark Falz", so it's got everybody talking that way.
He has literally no proof of this, it's just a big geometric shaped space ship that hovers, there's no way to tell what it really is, other than 'the biggest Dolls anyone has ever seen'. It winds up for a huge beam-blast so he mega-jumps to swat the blaster with his axe and is caught up in it. The trio had made it far enough away in time but, by the time you get up again the entire coastline is now missing and Aina was med-lifted to the city for her injuries. Mannon waited for you to get up.

You have to go with Mannon on foot to make the trek to the Central City to get to Aina and see if she's ok.
The town is literally gone and the coastline altered and blackened into an inlet, so there's nothing left to do there. Upon reaching Central City, a day's trek away, you're summoned by the current king-of-town / the mayor/leader guy Crawford. He's a soft-spoken, nice newman man in a fancy long white coat with glitter accents. He's a light beige color with a light purple-ish-blue to paler-blue fade short hair. He resides in a command-center type room with map globe, supporting technicians, surround-screens and a chair.
He explains that Aina is going to be fine, so she shows up about a second later looking for her father. Crawford has to tell her that they rescued some survivors, but he wasn't among them so he is now listed as missing. And.......she doesn't react. She's basically like 'oh well'.

I have absolutely NO IDEA why this bit is so apparently poorly done. The characters' faces don't change expressions much (in any circumstance) but they don't even narrow her eyes for this. Also, her reaction seems really badly scripted? And, it's not like they appear to be going for "She's in level 10 denial", because they DIDNT write her like she is. Even to someone who has to inspect humans for their emotions (or their apparent cover-ups of emotions) this whole thing reads wrong and badly done. It makes the entire interaction very confusing. It doesn't even go with the rest of the game, it's not like they're trying to make Aina a 'secret drone' with no emotions here, she emotes plenty later on about similar things so none of it makes sense. Hence, this aside

He basically asks you to look around the city, learn about it, take a rest, and then decide if you want to be on the anti-Dolls squad. Once out of the command room, Mannon brings up the commitment to fighting Dolls and asks if Aina is ok, but she's like 'nah I'm fine' (which feels a liiiiitttle more like a denial/cover up) to which Mannon reacts that she's "always bad at reading people or knowing their emotions". Mannon is one of these sorta 'deadpan' type girls, so that's fitting for her to react that way. Are they trying to code her as a tad on the spectrum? Or is something amiss with her (and she knows it) because she's a Meteorn?

Basically all 3 of you commit to fighting Dolls, so you're assigned to help a cast named DOZER (Japan may have had the character named Bruder (which would be pronounced brooder, but that appears to be the only changed-name in the entire game...which is fine.) on Mt. Magnus, a place known for hostile things and also Dolls.
On the mountain you have to fight your way up through various Alters, Lores and Dolls. Mt. Magnus is made of reddish rock and has various scrub vegetation that one might expect. There are rocky outcroppings and mini-plateau type areas. At the end of this journey is the main Dolls-badguy of the area, the Nogleth which is a quadroped type 'dragon' looking thing with no tail. It races around quickly and is probably about the size of a city bus. The limbs are the noodly gel. It has a heavily armored head. When it is badly damaged, it can go into a rampage mode where crystals come out of it and it does bigger attacks and goes wild. This causes Aina to freeze up, because it makes her have a flashback of the beam-shooting thing.
Dozer saves the day and the Nogleth is defeated. She gets super upset that she froze up, and recalls how her dad sent her away from the beach attack 'because she'd be in the way'. Dozer has good advice though which is that it's ok to be afraid of the Dolls but you have to attack them anyway, like he does. (Bravery is, by it's definition, being afraid but acting anyway for the greater good or saving people--even if the one you save is yourself.)

Later, she thinks about quitting, and summons you and Mannon to talk about it.
She is talked out of this fairly quickly though
. So, shortly after, (the next day) a call goes out to help at the Vanford Labratory Ruin, which is a place that the Dolls destroyed maybe 30 years ago or so and nobody ever re built it. The trio (you, Mannon, Aina) agree to go, which inspires others to do so as well. There, Dolls are of course on the rampage but they are backed up by a big energy glob that blocks communication. This turns out to fall down and form into the Daityl Sword, a very tall and lanky biped / somewhat humanoid thing. It's probably 3 or 4 stories tall, so, building height. Beating him in the toes is something he hates, so you can defeat him.
Once the Daityl Sword is defeated, another call comes in that Dozer's squad went into the Resol Forest Area and now appears to be in trouble, so you are urged to rush there next.

Though, you probably can't.
This is where the game's actual mechanics comes in, which is "Battle Power".
Anyone not totally ignoring the story to go zooming about the countryside defeating any and all things will likely not have the Battle Power to do anything yet. The Ops girls will call you and a new 'main quest' will appear which is to talk to some NPCs and raise your BP to a certain amount before the forest can even be entered at all. You basically have to run around until you get to Level 15 or so, grind whatever 2nd or 3rd teir weapon you have up past 20 or so, run every single cocoon & spend every single Skill Point (from those cocoons), as well as performing at least 1 weapon "limit break", and making your main weapon a "combo weapon". All of which is very expensive to do, so you will also need to red-box hunt (There are 113 of them in the 'chapter 1' area that this takes place in) You do have to work at it to be able to reveal more story.

The Resol Forest
This forest has giant trees, glowing mushrooms, steep hills and twisted roots everywhere. Sunlight only filters in a little bit. There's lots of moss and rocks and some plants that glow a little. It is a nifty place to see. To start this quest, you can meet Aina outside the forest border, and go inside. Mannon then arrives and tells you that there are three signals that could be Dozer, so there's nothing to do but investigate each one. The communications in this area are blocked, just like they were at Vanford. So, you have to get in there and defeat various Oodans, Pettas Axe, Pettas Launcher, and other regular area Dolls. Running from marker to marker, you still can't find Dozer.
Eventually, there's a larger clearing where you can spot what looks like a guy standing there. Two people escape, the Techer & Ranger from Dozer's squad. The guy is metallic looking, and isn't facing you. He's perhaps 1.5 regular people tall, or a bit taller. This is not a person though, it is a new type of Dolls, the Bujin. You don't get to inspect it though, because Aina and Mannon will attack it from afar and set it off. Look carefully at the Bujin, it only has one arm. Why would they build it with only a single arm? It has a long katana that glows with energy when it is getting ready to attack. It has many powerful attacks like turning invisible, multi katana slash, shadow-clones, shadow-movement, a huge AOE dome of doom attack, airial juggles and more.

If you can defeat it...
Another signal will appear and Dozer sure won't. It was not the Bujin that was keeping Dozer from everyone. Crawford will call you, saying maybe you should retreat because there's a big signal in the sky that something's coming down. No one will leave though, so you go to the next coordinate. There, the bad Dolls dragon @@@ appears. This is a rather "S" shaped winged dragon thing with a long curved torso. It has smallish wings, a long tail, and both hands/feet. It can breathe fire, slash the tail, spin attack and fly around. As you fight it, Dozer shows up to help out, but tries to scold everyone for going into the dangerous Resol Forest. He clams up though once Aina yells how determined everyone is to save him.

Dozer says there's no point in running away from it now (as it flies and is fast/it won't do any good) we've got to try and defeat it. It's turning radius isn't that great, so trying to stay under/at the back feet works pretty well. Eventually Dozer can blast its tail off. When it gets low on health though, watch out! Just like the Nogleth, the @@@ will turn red and go into a rampage mode. This mode includes growing 2 more heads for a total of 3 attacking heads. It can also do ground/flame attacks, falling fire meteors, area burn, energy blasting and pillars of fire from the ground.
The characters will mention that it has "Cores" in it, and, indeed it does there are two yellow glowing round....disks? Embedded in the torso area that are especially vulnerable to attacks. In this case, the NPCs are actually pretty helpful in battle. They never die of attacks, and they are able to do ok damage.

Of course, this freaks Aina out, so you can say

Remember What Dozer Said
We've Got This Aina

If you say We've Got This Aina, she looks around to see that you, Mannon & Dozer are really there to back her up and has a vision of her father too, (a flash) and is able to stand and fight even though the thing is going wild. There's a cinematic type that shows each character doing a cool attack against it, and the dragon is defeated. She tells Dozer that his advice really did help, Mannon is clearly proud of her, and everyone is happy/relieved. The @@@ was what was blocking communications too, so as soon as it's gone, Central City's calling you. He's amazed you could beat it, super happy to see Dozer again and that everyone's fine. Everyone agrees to go right back to the city.

Once there Crawford tells the ops people that "The Materials were gathered successfully." Aina asks what about that? This forces him to explain what Dozer was there to do. (He's embarassed she caught him out on this, he clearly didn't want to explain his ideas to 'the newbies in town', but.....he's no seasoned politician! Embarassing him/calling him out actually DOES work, and he feels bad about it enough that he'll explain...nice) It's that they need items from the dolls themselves, and various areas of the planet. As you know, people are rich in photons, but what's richer is the planet itself AND the atmosphere. The Garou vs Falz attack has been studied, and it's determined that the photons of the people/place harm the Dolls. Garou had the right idea, but Falz was just too big (giant metal space ship) for his photon attack to strike the core.
So...what if the atmosphere's photons could be collected instead for a giant attack to defeat a giant thing? The idea for that is called "Central Cannon", but it can't be completed without more items from far and near. Do you want to be part of the item gathering force that goes and contacts other Arks/people far away? Aina assumes this means we'll be his gophers/liasons to try and persuade strangers to help Central City. He says that's about right, and all three are signed up to the job.

End of Chapter 1: To Be Continued...

Preview: A sandy area is shown, where a menacing Dolls sand-worm is obviously lurking

1. Why does nobody ask about the Bujin? It is the only Dolls that looks like it is trying to be a person.
2. WHO is building the Dolls? They are obviously artificial constructs, not 'wacky animals Falz is making' like every other time.
3. Some Dolls are apparently very old, when you see "Veteran" Dollsname, they'll have moss and dirt accumulations on them. Where were these hiding that nobody stumbled onto them? You always encounter Dolls while they are wandering around, they never spawn such that you can see them 'appear'.
4. The expensive item "Alpha Reactor" looks suspiciously like something that's sometimes embedded in some Dolls.
5. The "Guarded/Boosted" Dolls have a glowing yellow cylender embedded in a sharp/twisted 'barb' that is stuck in them. It looks like they have been stabbed/pierced with this to injure them. (Ex. in a Doltz it's jabbed through the joint of a back leg) Breaking the cylender makes the Dollz vulnerable to attack....but then why was it stabbed into them in an injuring way?
6. What causes "silver and gold"?
Dolls, Alters, Tames, and Legacy type anythings can appear in 'silver and gold' colors where it looks like they were dipped in chrome. If a Dolls is a metallic color it will be stronger than normal and have more HP. It does not seem to be the case for anything else. Of course, they drop more/better stuff but...what causes the coloration? The animals don't seem to mind.

The characters will talk about the eerie forest, but they won't remark on the cleary-person-looking-ninja?
Why don't they talk about the Dolls in general more? Nobody asks Mannon what she remembers as a Meteorn?