I always felt like Perfect Works is talked up too much and it seems it often comes from people who haven't actually read the fan translations. There's not much to be intrigued about, it tells you what each episode is and most of them are just the different eras Xenogears's plot goes through. Ep.2 is the spaceship carrying deus crashing in the opening animation, Ep.3 is Kim fiddling around with nanomachines in the Zeboim era, and Ep.4 is the story of Lacan and Sophia. It's just the stuff we already see in Xenogears.
And a lot of the Xeno games have past events shown in flashbacks. By Perfect Works' logic, Xenoblade 2 is three episodes in and of itself: Ep.1 Klaus and the Zohar, Ep.2 Torna, Ep.3: The Story of Rex. Xenosaga would be structured like: Ep.1 Grimoire Verum and the Zohar, Ep.2 Pied Piper, Ep.3 The Miltia Conflict, Ep.4 The Story of Shion.
Episodes 1 and 6 were really the only ones that he seemed to have an intention of turning into full games, one prequel, and one sequel. Episode 1 is about how after the discovery of an alien artifact, civilization rapidly advances (a la 2001: A Space Odyssey) and ultimately builds a superweapon and the Galactic Federation has to offload onto another world to get rid of it. So the idea is Xenosaga is a reimagining of episode 1 and it would lead up to a new version of Xenogears as episode 5. I believe that's legitimate up to a point. I think Perfect Work's episode 1 was the basis for Xenosaga, but it lacks the most important aspect: the building of Deus. It's possible plans changed and Xenosaga was evolving into something else had it continued.
But something that peeves me is the constant claim that every new Xeno thing is an episode and proof the Takahashi is retelling Perfect Works and trying to Trojan horse its way through under Xenoblade's success after Xenosaga's failure. When X was coming out, people were like "oh it's the Eldridge crash, he's telling episode 2!" okay, so where's Abel making contact with the Zohar? Where's Myang and Cain? Is the lifehold Deus? Seems like stretching. And of course it's been pointed out the xb2 is a retelling of Xenogears and Torna is episode 4. That's fair, there's a lot to compare, but now I've seen people on other sites saying "there's two nations at war that start with K and A, it's episode 5!" Okay, but you've been telling me xb2 is Ep.5. How many episode fives does this story have? Even with xb2, while's there a lot of comparisons, there are also a lot of comparisons between gears and saga's story structure (look at this:
http://xenogearsxenosagastudyguide.blogspot.com/p/xenogears-and-xenosaga-mirroring.html) yet no one says saga is episode 5. Soma Bringer's the only Takahashi game that's escaped this even though it's Xeno as hell (it's a Takahashi helmed project, with a script from Soraya Saga, and music from Mitsuda) just because it doesn't have Xeno in the title.
I think people get way too hung up on how Takahashi described Xenogears's flashback eras in a materials book 25 years ago. That's the other thing, it's just a material/art book. That's all Perfect Works is. Some fans talk like it's a series bible but the section where the six episodes are described is just one tiny part of it. I'd argue the bestiary where they give in-universe explanations for the various monsters and how they evolved is vastly more interesting than just describing the eras you see in flashbacks as other episodes. So, the Xenoblade games already have their own Perfect Works. Materials books have been released for all of them: Monado: The Secret Files, The Art of Mira, and Alrest Records.
What I think it really comes down to is that Takahashi just has a set of interests, concepts, and obsessions that he has fun writing about and likes to put in his stories. I honestly believe it's that simple. It's more like Yuji Horii reusing a lot of narrative ideas across all the Dragon Quest games. The high concept framework of xb2 is similar to gears, but the actual story and themes told within that framework are xb2's own thing.
I don't mean to tell anyone they're wrong or spoil anyone's fun speculating about connections, but I do want to throw out another way of looking at Perfect Works. I've seen Luxin's videos talking about perfect works and he almost seems dogmatic about how Takahashi is definitely retelling Perfect Works and how the gnosis are super important to the future of the series because ideas of how they function were reused for the Fog King. It's easy for new fans to get sucked into this as truth without even reading Perfect Works or finding out it's just a materials book, the episode descriptions are just one small section, and 4 of 6 episodes are just the stuff we already saw in Xenogears. That's how I was when I dug into the series after falling in love with Xenoblade 1 until I actually read Perfect Works.
It might be healthy for the fandom to not revere Perfect Works too much. Episode 1 is the same way every Takahashi thing starts - a Space Odyssey homage - and episode 6 is just "we can't tell you yet!" sequel tease that says nothing (and I wouldn't be surprised if he never actually had a concrete idea for it), and the rest of the episodes are what we see in Xenogears. It's not that interesting despite how much people hype this thing. This idea that Takahashi's been trying to tell the same story for 25 years really sells him short as a writer.
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