* This was supposed to be the fifth episode of a six-game series, and Xenogears Perfect Works covers what would have happened in the first four episodes...but where the heck would the developers gone with episode six? I mean, by the end of Xenogears, Deus and its servants are all defeated, Fei and Elly have regained the memories of all their past lives, the Wave Existence is freed...simply put, there are no plot threads left to resolve in a sequel.
** The Perfect Works says something about how they hinted at the first four episodes in this game, with the implication that they knew I-IV were going to be cancelled. Maybe the original ending was going to be a cliffhanger to segue to episode six, until they squished it into this game, knowing that the others were cancelled?
** Perfect Works makes a huge deal about Deus wanting to find Earth, so episode six might have dealt with that. The ending of the Xenosaga series points in the same direction.
* What was the point of the villains crucifying the heroes, and by crucifying them, it's putting their mechs on huge crosses. Presumably the heroes are just sitting in their cockpits comfortably while their mechs are nailed to crosses.
** One word: [[WebVideo/BadMovieBeatdown SYMBOLISM!]]
* If Citan knew what was in the Soylent food, why didn't he tell Fei and Elly before they ate it? Some kind of sick lesson to be learned?
** They were really hungry and he probably didn't want to spoil their appetite. I'm not sure which is worse though...
** Like Citan said, they've already eaten the stuff before via medicine and food supplied to the world via the Ethos. This goes double for Elly, who being from Solaris, has probably went her whole life eating nothing but recycled food.
** Yeah but he still could've stopped them and THEN show them why. All this does is show him being an ass for no reason. Plus it carries the HUGE implication that Citan knew all along but still ate and used the medicine just fine.
* What the heck does "Small Two of Pieces" (the song title itself, not the lyrics) mean?
** It's a reference to a part of the game (in Shevat, I think) that humanity is compared to the pieces of a broken mirror. The song's title is an artifact of the original lyrics, which were much more engrish-y before Joanne Hogg rewrote them.
* Here's one that always bothered me. The dramatic reveal that Fei is Id, is begun when Weltall activates on it's own, turns into Id mode, and breaks out of the Yggdrasil, triggering an alarm on the bridge which alerts Siguard. Well and good, except that earlier on, when Id awoke to confront the team at the Zeboim ruins, it not only did this, but also returned to Yggdrasil afterwards and settled back in in the hanger (Weltall is shown with steam coming from it's vents when the party find Fei here) without anyone on the ship noticing. Huh? What did Id repair the hole before switching Fei back in? Did nobody not notice a gear leave and then return on it's own. Did nobody notice a gear in the hangar suddenly go missing for at least 20 minutes? Or the gaping hole in the ship? Or did Id somehow politely ask someone to open the hangar and nobody wondered who this strange guy was? This just...doesn't make sense.
** It's pretty well established in the fandom that Fei = Id wasn't supposed to be that big of a reveal. Blatantly obvious basically.
*** Except it was pretty obvious that it ''was'' a big reveal for the characters. The issue with this is that, whether the player figured it out or not, the ''other characters'' should have figured out what was going on when Weltall left the Yggdrasil to confront the party in the Zeboim ruins, and it was clear that they didn't.
* Why are the save points called Memory Cubes when there are so clearly not cubes?
* What was Deus' original goal? After reading Perfect Works, it states that when he took control of the Eldridge, he did so with the intent of going to Lost Jerusalem, A.K.A. Earth. But what was the reason he did this?
** I always saw it as this. Deus is a weapon of mass destruction. No matter how powerful it becomes, no matter how much it evolves, it's still a weapons system. It was going to go to earth to kill everyone there because they were trying to deactivate it, and it saw that as a threat, and in it's programing, threats must be destroyed.
* It bugs me that so many people think that Billy actually became a prostitute for a while to when he was strapped for cash. Billy states, quite clearly, (and this is in a game noted to not be very clear all the time) that he CONSIDERED turning tricks for cash, and NOT that he actually did it. I'm not even that big of a fan of Billy nor do I think prostitution is all that shocking or whatever, but it kinda irks me to see it asked or stated constantly that Billy is, or was, a prostitute.
* Why does Khan disguise himself as "Wiseman" ? His goal is to fight Grahf and to make Fei strong enough so that he can resist Grahf, and also follow his destiny as the Contact without falling to the machinations of various big players (Miang, Krellian and the Gazel Ministry mostly). I don't see how anything of that could get worse if Khan just told his son he is his father and helped him in a more direct way. Sure, Khan unfortunately has other things to do than caring for his son, and it is quite understandable he doesn't want to be around his son on a regular basis in order to protect him from Grahf. But why the mask ?
** Because if Fei knew he was his father he'd likely chase Khan regardless of the danger out of desperate desire to know about his past, which could risk both appearances of Id and Fei being in Grahf's clutches especially since it was important that Fei not know about his past until everything was in place for him to merge with Id. Better to be a mysterious man with no apparant connection to Fei who Fei has little interest in seeking out (since while Fei appreciates Wiseman's occasional aid he never actively tries to find him) than saying "Fei I'm your father and I can tell you everything about you you wanted to know but I can't because you'd be in danger so just aimlessly wander around with your new buddies and try not to get too angry. Later." and hope Fei was mature enough to accept that and not abandon his quest to chase him for answers. Or worse have to tell him "Well ok you actually have a psychotic alternate persona with WMD level power and you were the one who killed your mother and destroyed your adopted village, and destroyed your new pirate bro's ship and also you've destroyed entire cities under Grahf's command." if Fei just won't take no for answer. That alone would break Fei and either drive him into a coma of despair or worse wake Id up for some murder sprees and that's before he gets into them being the Contact who has to oppose a machine god.
* Where do Id's clothes come from anyway?
** [[WordOfGod According to the game director]] in the [[AllThereInTheManual Perfect Works artbook]]... [[ShrugOfGod he has no idea]].
** [[VideoGame/MetalGearSolid4GunsOfThePatriots NANOMACHINES!]]
* While I admit that the final boss Urobolus feels pretty damn good seeing as you know it's really Miang. But why was she so dang easy? Was it because of the whole Disk 2 fiasco, or was it plot-related?
** It was probably one of those final bosses that opted for more of a storyline-take on it like many other games of the time period, such as the strikingly-similar ''VideoGame/WildARMs2''. Also, consider the fact that some players defeated a [[MarathonBoss marathon of five bosses]] beforehand, so making Urobolus tough would have been a little overkill.
** Also, Miang is part of Deus, and Deus just got a butt-kicking from Fei & company about a cutscene or two ago. She may have had barely enough power to hold herself together, much less put up another fight.
* Why do Billy and Tolone have the same face?
* How much of the modern technology on the Xenogears planet is scrapped from Eldridge wholesale, and how much of it are parts disassembled from Eldridge ruins, and how much of it is built be the humans themselves? For example that room with the computers underneath the Ethos headquarters, was that a room from the Eldridge and the HQ was built on top of it, or were the computers brought over? Or the Zeboim ruins Fei and co. visit, were all those buildings on the Eldridge?
* Why could only Ramsus kill Cain? Why couldn't anybody who was powerful?
* If the Gazel Ministry and Miang and Krelian all wanted to resurrect Deus why would they possibly start and perpetuate a war between Aveh and Kislev? Why would they do anything that would lead to a reduction in population?
** The war perpetuated them to constantly dig for artifacts like Gears. The idea was to use them to try to find the Omnigears.
* Why didn't blowing up Solaris stop the Solarians at all?
** Because all it really did was blow up all their civilians. The majority of Gebler was already on the surface and all the important Solarians escaped. It really just made them worse since they had no civilian populace to have to keep content anymore and the soldiers and ministry could just go wild.
* If the Wave Existence created Elly, then why can she also be overwritten by Miang?
** It only created the original Mother from Abel's wishes. After that, she was basically split into two: Miang and Elly. Miang was under the control of Deus while Elly was compelled to always partner with Abel and his reincarnations.
* Why did Citan wait until after Fei and Elly ate the Wels meat to tell them what it was made of?
** Maximum drama. Maybe to really hammer into their heads how Solarians truly live, but it still makes him come off as a jerk.
* How did Fei/Id sneak out of the Yggdrasil without anyone noticing when everyone was collecting Emeralda?
* What was the original purpose of the giant mirror on Babel Tower? I don't believe Citan is correct, because I find it hard to believe whoever designed the Eldridge would create a weapon based on bouncing a laser off a mirror when it already had rotating lasers turrets. Also, from looking at the Eldridge, it did not have any parts that stuck up besides that slanted fin in the back, so Babel Tower must have been a part of the Eldridge's exterior, or inside the ship.
** It's likely it was originally a focusing lens to concentrate laser fire to be more powerful.
* When and why did Bishop Stein's face melt?
* The entire point of Miang and the Gazel Ministry killing humanity over and over was to create spare parts for Deus. But how exactly were they getting these parts to Deus in the first place? Keep in mind Mahanon, the large part of the Eldridge that sunk into the sea containing Deus hadn't been raised for nearly ten thousand years. So how could they have been sending said dead humans TO Deus?