Since the thread title contains a spoiler warning, I won't be blacking out the following text.
It's been a while since I completed the final two chapters, but I'll fill in what I can.
* You escort Dr. Tomrain to the Kugu RELICS on Moatoob to make the final preparations of the confinement system located there.
* Hyuga assume his position as president of GRM following the removal of the previous ownership thanks to their involvement with the Illuminus. (He ends up using his power to fund the production of numerous generators which will be required to power the confinement systems.)
* After the confinement systems are ready on the three planets, a trip is made to Rykros to get the fourth system set up for the big day.
* Before this, however, Helga kills Dr. Tomrain and kidnaps Lumia. It should also be noted that Lumia has become very attached to Tomrain, looking up to him as if he were her grandfather. Likewise, he had become very fond of her.
* Upon arriving on Rykros, we find out (from Karen, I think) that the SEED were created by Dark Falz.
* The resurrection of Dark Falz was the Illuminus' plan all along. Dulk Fakis, it turns out, was essentially a prototype Dark Falz.
* Dark Falz had been sealed away by the ancient civilization of Gurhal, but when the confinement system was reactivated at the Unification Point in
Episode 1 to seal away the SEED, this opened the door ("The Gates of Denikaya" I think is what it was called in
Episode 1), so to speak, allowing Falz to begin its escape.
* All four confinement systems are activated at the new Unification Point, destroying the SEED and their HIVEs. The weird spots that were covering the sun are also lifted by the system. (At this point, the sun was pretty much blacked out with sunspots.)
* With the confinement system open, Dark Falz fully escapes, and a battle (against its second form) begins.
* Once Falz is defeated, Rykros begins to collapse on itself. Your character is forced to escape to the Landeel, leaving Ethan and Karen behind. At this point, Karen had collapsed from exhaustion. She was already worn out from using her abilities to activate the confinement system, but the Falz battle tapped her photon energy, it seems.
* The next scene shows the Landeel flying away from a dying Rykros. The planet begins to crack apart and collapse into nothingness.
* You wake up on the Landeel, surprised to be alive. Of course, the mood is pretty somber as everyone believes Ethan and Karen to have died with Rykros. But, that was not meant to be. Turns out that Mirei had been watching over them. She had cocooned them in photon energy to protect them from the planet's collapse, and flew them to safety.
* Ethan and Karen fly through space talking to a large manifestation of Mirei which is congratulating them on vanquishing the SEED. Mirei then disappears and the two of them fly to the Landeel.
* The following points relate to the Lumia kidnapping subplot.
* While on Rykros, but before activating the confinement systems, you get a call from Helga. She uses Lumia as bait to get you to go off on your own into the Rykros RELICS. You get to a dead end where you find Howzer (still quite alive). He traps you in a ridiculous field of lasers and then does his floaty-laser-cuffs attack to kill you. (The screen actually fades red and "Sadness" plays in the background, as if you've failed the mission.) In the next scene, you are resurrected by Karen.
* Cut to Helga and Howzer standing over Lumia on the raft where Falz's first form is fought. They begin taunting Lumia over how Tomrain is dead and how your character was just killed, etc. What they're trying to do is piss her off enough to get her into a dark, depressed state of mind. Of course they succeed, and then Helga transforms into SEED-Helga and fuses with Lumia. (Visually, she looks just like Lumia after the fusion.) At this point, you, Ethan and Karen show up and there's a battle against Falz, which I think was resurrected using Howzer, Helga and Lumia all as hosts.
* Once Falz is defeated, Karen is able to sense Lumia's presence. It turns out that she still exists in the consciousness of Dark Falz. Her location manifests itself as the ruins from
PSO.
* While in this state, Lumia is able to communicate through the void, though it does become a strain on her. She knows this and tells you and your party that she doesn't believe she'll escape. But despite her impending fate, she assures you that she's not crying. She remains strong of heart and is happy that Gurhal will be at peace.
* Somehow you are able to enter Falz's consciousness to rescue Lumia. You run through the four areas of
PSO Ep.I until you find her standing on an altar in the ruins doing her best to concentrate to speak out through the rift in space. You speak with her and eventually get her to come back with you.
* After this, I believe the scene cuts to a month or two later. Lumia is talking with Mina at GUARDIANS HQ, and you walk up to her and go out on some mission together.
* Now we get to back up a little bit for another subplot. In this one, you can have Lou accompany you on the trip to Rykros. It turns out, though, that this is actually Vivienne who has body-snatched Lou. (Personal hacking, I think it was called in
PSP.)
* In this subplot, you can get Magashi to join you, so that it's you, Vivienne and Magashi against Dark Falz. Vivienne fills the role of Karen as being able to detect Lumia's presence after the fight, and then you go to rescue her.
* One little random bit of trivia: the Vol Bros. reveal to you (in their subplot), that after all of this is over and Gurhal is safe, they plan on opening up Casino Voloyal.
Really, I suppose there's a lot more to this than what I've said. (Though, that is a pretty massive wall of text up there.) It's been a while since I last played the story missions, and even then, I was jumping back and forth from subplot to subplot to get partner cards, so I might have some details mixed up or completely left out. I don't plan on playing the story missions again too terribly soon, but I will get back around to it as there's at least one more subplot that I haven't completed. (I just need to figure out what one thing I'm doing wrong...)
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