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PSO2 Story Guide
The story of PSO2 has many chapters & is very 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.
Character Guide
Planets/Areas Guide
Special Quest Mission Write Ups
Color key
Green Text: Speculation
What You Do/The official "Party Line" appears in RED TEXT
Bold Text: Important information
Choice Options: Blue Text
Dates & Times (Story is time travel related) Purple Text
Story Guide HUB

Zeig has discovered the item you brought him really is a weapon, and he estimates there should be 2 more pieces. (How does he know how many pieces something broke into? He could have half, or the tip could have shattered into 100 and how would he know?) He says he could extrapolate maybe how it went with replacement parts, but that wouldn’t do it justice…so it would mean a lot to him if you could find the other pieces.

Theodore is in the volcano on this day too, but he’s doing better. He confesses he’s still doing the bare minimum, and getting better at pretending to fight, but that’s actually working out for him now. He says if he told someone more serious, he’d be fired, and that won’t do cause he doesn’t work well outside of Arks…nor in it. He says even if he has the talent, it’s not in his personality, but that ‘his friend’ (it’s Ulc) would just say to be more serious.

Ulc however, is not having a good day. She found out that even to be in a non fighting/secretarial (or other clerical) role in Arks, those who have photon proficiency get hired first, because in an emergency, they could still be sent out. She feels defeated, until she says ‘not trying is the same as failing’, and admits it only makes it harder to get hired, not impossible. She vows to do her best.

The following day, Zeno appears in the lobby to ask what Zeig wants, saying he’s a troublesome geezer when he gets worked up. If you tell him it’s the weapon piece from the Tundra, he has suspected it is so. (This is logical, the only thing that gets Zeig doing anything is weapon-related) Zeno tries to be helpful, telling you that there are clues about where another piece could be: because searching darkers & Mask-Man are apparently after it, going to where they are/were would be the place to start. (Really? Because if they’re already there, or have come and gone, wouldn’t they have gotten the item? Plus, nobody even knows who/what these are, so they can’t be predicted) He’ll let you know though, if he hears anything.

Aki calls, saying she needs more data and wants you to go to the volcano Amduscia caves with her. This foreshadows the story chapter quest that comes up later.

Rogio calls back, as promised since he’s learned more. He says the tundra is 100% unnatural, but has no idea of the cause, but it wasn’t a meteor. He feels something may be jamming his signal, which makes no sense because Naberius was supposed to be wild/undeveloped planet.

Chapter 4: The Dragonkin's Disease - The Scientists State

3/19 at 1200
Aki and Light are waiting in the caves. She says no explanation is really needed, so neither is small talk, let’s go, and sets off. Light apologizes for lack of an explanation, saying he hopes the investigation doesn’t get out of hand like last time (when she just disappeared) and if it does, you & Light may have to just grab her and retreat. She returns to the conversation asking you to destroy as many darkers as possible, so she can gather data about how darker particles interact with what’s around them.

At 1220, Aki complains that taking out darkers is taking up time.
She states that there have been more darkers down here lately, but also that the dragonkin have become hostile toward Arks. The Arks had translated the dragonkin language, and had been interacting with them for some time, but now, none want anything to do with the Arks. A dragonkin Sil Dinian wanders up, but he has a clear darker infection point on his chest. (Radiating type)
Aki wants to talk to him though, and introduces herself with a “hey you”, however, when he growls back, it’s heard in everyone’s head, rather than out loud. (They are psychic? Yes sort of, their mouths don't move when they talk, so how does one even begin to translate a psychic language? Whatever the answer, ARKS pulled it off long ago.) He attacks the party because he is infected and so you have to kill him because he is like a zombie.

At 1240 Aki finds a dead guy dinian
Light is disgusted by the prospect of a corpse and doesn’t want her to touch it. She of course, touches it anyway. (And presumably cuts it open to see the organs inside) Much to Light’s disgust, which she yells at him for, because he won’t stop saying eew to it. He is posed/animated like the dead guy stinks a lot, although it just looks like a laying down dinian. She finds that this person was accumulating darker infection inside. She explains that if darkers are killed with non photon weapons, they’re not completely destroyed. Her analogy is ‘if dust is left behind a mountain can form’.
She got the data she came for though, but recognizes that if Arks can’t talk to dragonkin, it’ll all be for nothing, so your objective is now to contact dragonkin. (So, presumably, this dead dinian killed darkers/darker, with his natural sword & spiky shield, then because they were non-photonic, he became infected by the ‘darker-dust’ leftovers) She encourages you to keep to the north of the map the entire time. If you do, you’ll eventually reach…

At 1330 After passing a key trap…
You encounter Hi En getting ready to fight Hi Loga, a Vol dragon. Hi Loga has a round infection point on his face. Hi En is a healer-type dinian (so how was he going to murder him?) Light is surprised to see them getting ready to fight each other. Hi Loga will only roar, not speak.
Aki offers to help out, but Hi En just tells her to go away. Fortunately, she persists, saying what will you do, kill him? Hi En says yes, because he’s broken some sacred laws and must be sent to hell with Kashina, the hell-dragon. (even though he is the paragon of the Hi clan) 
Aki asks him to let her team give it a try, to destroy the infection with photonic weapons, and maybe he won’t die. She says he’s not himself. (Which is 100% true, it makes anything crazy and evil without thought once infected)

If you can beat this vol dragon by hitting the infection point, he falls down, but is ok. Hi En goes to him, and he is confused, but talks a little. Hi En says it’s the power of the Arks, but Aki reminds him this could be just the start, not everything’s so easy to cure (and he got some hits, but will heal quickly) so if the dragonkin don’t start communicating and changing some things, it could get worse. Hi En realizes this, and says he owes you all for saving Hi Loga, and is grateful. They both leave, and you can collect the crystal & end the quest.

Proud Scales of Amduscia 3/19 at 1220

This is the timeline that DOES NOT happen. The original one, where you listen to Aki about going north & save Hi Loga is the one that actually occurs. It starts off exactly the same. However, when Aki tells you to keep to the north, do the opposite. Cling toward all non-north walls & go through south gates if there’s ever a choice. This will lead you into a different path.

Aki says the dragons are strong but you're good for dealing with them easily. They're aggressive lately but it wasn't always that way. She sees a dragonkin, but unlike the other path/first path this one isn't infected visibly. She says he'll see you as a threat so leave this up to her. Their language was translated by ARKS so we ought to be able to understand them. She calls out, by telling her name & asking if he'll listen. He runs away, which she takes as that he does understand. She feels clearly ignored, which irritates her. She laughs and says it makes her want to communicate all the more!

Just wait! He'll soon see how hard it is to ignore her. Light calls after her, but she's run off. He wonders why this guy didn't attack. You give an answer (mouth moves, no word) Light says he doesn't know what you mean by "playing it cool". But while we talk she's getting further away, lets just go. What indeed does this mean? Let her do all the running around and pestering of these aliens?

In the next area, you can find several different groups of dragonkin fighting a few darkers to illustrate the conflict. There's also a code elimination for infected dragonkin.

at 1240
Aki is worried seeing so many darkers. Light asks it could be ok because the Dragonkin can defeat darkers on their own? Aki says supposedly so and that's why they have a policy of trying not to interact with ARKS. Aki is trying to warn them of the dangers of that policy because Darkers can only be permenently destroyed with the photon weapons of ARKS. The dragonkin brute-force way of beating them isn't enough because it leaves residual fragments that spawn more darkers later. She believes it has something to do with why they're attacking the ARKS, but without some cooperation she can't investigate. That's why field work has to be done in person.

at 1300
The next area isn't big and only has some darkers and 1 code collect. After it, a Vol Dragon appears. Aki says that it's said that Dragonkin posess more knowledge than humans...but looking at this sad dragon slowly dripping flames from its mouth as it stands in a cave, she finds it's hard to imagine that is true. (It is indeed not true)

He Looks Like He's Angry
He Looks Like He's Crying

If you say He Looks Like He's Crying, Aki says a poetic expression but not bad. Light says its not the time to talk as it's coming this way. The dragon yells and you have to fight it. The code is defeat the Hi Loga. (So this IS the same dragon—just this time he dies because it’s the wrong path/the timeline that ends up not happening. Hi Loga being infected visibly is what saves him in the 'correct' timeline. WHY he attacks here/looks sad/sick is unknown. They don't talk or explain anything this time, like they do on the right path.)

Hi En rushes up and says 'its too late'. Aki hears a voice echoing in her head, and asks him if he is a dragonkin who understands our language. Would he hear us out? He refuses, telling you to go back as there's no use for words with ARKS. Aki apologizes for having to fight with the kin...but if he's actually intelligent he'll realize that something's amiss here. A normal dragonkin like him, just doesn't attack on sight...correct? He doesn't want to hear it though, saying he's no interest in word-games and runs away. (Your team just killed their 'paragon=leader dragon' so Hi En is too distraught and will only return with bad news about all murderous ARKS. She's destroying the communication attempt here.)Aki protests, but you reach out to her, stopping her. She realizes it's enough and quits the mission to head back. You now get Aki & Light partner cards to summon them at any time for solo missions.

This is the BAD END version of this chapter.
Hi Loga dies & Hi En won't talk.