Rui was kidnapped in Pyrite Town. The goons then travel to the Outskirt Stand, and then to Phenac City. But... the Outskirt Stand is further from Pyrite than Phenac...
Maybe they missed it? I mean, Orre is a giant desert after all. It's possible they could have gone so far off track that they overshot Phenac, and only found out once they reached the Outskirt Stand. They're certainly incompetent enough to do that.
They're eating there. They said.
They never kidnapped Rui in Pyrite Town, they discovered her there, and chased her to kidnap her, so they most likely had to chase her past the Outskirt Stand where they captured her and then decided to stop for lunch.
Actually, no-one ever said that. She might have been kidnapped in Pyrite. But they specifically say they've just eaten, after walking out of the Outskirt Stand.
It personally just bugs this troper that so many people consider Shadow Pokémon to be the spawn of Satan. I mean, seriously, they're controllable and they don't attack your Pokémon. They listen to their trainer when they go into Hyper Mode, a mode that is explicitly stated to be an emotional high. Their attacks still only faint an opposing Pokémon, even if you use a Shadow move. They relax when you give them a massage. They clearly respond to affection by reopening their heart. They're not soulless, nor are they bloodthirsty maniacs. Hell, the worst we actually see is a Makuhita punching (well, it's implied anyways) a human (although, admittedly, I've only played Colosseum. Maybe XD changed things).
Shadow Pokémon are probably like this cat: only "evil" because they've been abused to the point of oblivion and dangerous and repellent to human affection because of it. I imagine they're basically like dogs that would bite your hand off because they assume that any attempt to touch them is an attempt to hurt them. Purifying is equivalent to readjusting an abused animal to accept affection and whatnot.
That interpretation doesn't quite work, considering you can take a freshly snagged Shadow Pokémon and start massaging it until its heart reopens. And (from what I've seen), XD just had you sticking them in purification chambers.
It's touchy territory with you, so I'll try to explain it away. From what we've come to know, Shadow Pokémon are to be pitied, as Prof. Krane put it, due to the fact that they've been subjected to explicitly objectifying abuse to a point where they'll snap at anything around them or obey any command, no matter how vulgar, to get the pain to stop. Exposure to beings of compassion (regular Pokémon in the Purification Chamber, or the good (even if not on the surface) trainer that Snagged them) is meant to reopen the Shadow Pokémon to the world in a metaphysical and/or emotional way. They are probably instructed via the Ball they are confined to that their trainer is the only person who understands them, though this compulsion is a restraining bolt to keep a Shadow Pokémon from causing harm to Cipher. This mechanism also explains why stolen Cipher tech (the Snag Machine in particular) is an absolute requirement to purify them ("While the act of stealing another trainer's Pokémon is unforgivable, there is no other way to save Shadow Pokémon"). Then again, Shadow Pokémon by themselves are inherently neither good nor evil, even if they are imbued with evil power as a weapon for Cipher. I guess the desire to use such evil power regardless of how the Pokémon was conditioned is a side-effect of The Corruption - that it empowers the trainers using them to commit evil.
Okay, so you're saying XD explained most of this stuff. Grand. Also, last time I checked, Poké Balls (except for the anime-only Dark Balls) contained no slave programming whatsoever. The Pokémon you catch listen to you because you proved to them that you were stronger than them in a battle, and they will listen to you so they can become stronger as well. Finally, this doesn't answer my JBM at all, because it seems that even though XD explained things a bit more, there still seems to be no basis to Shadow Pokémon being portrayed as absolutely evil Pokémon.
"Obey any command". They don't care who is giving it.
It's due to the state of the Pokémon; not the Poké Balls they're in.
Also, Gameplay and Story Segregation explains away this whole problem. The story is that Shadow Pokémon will attack anything, even people. I imagine that that would be fairly difficult to deal with in-game, and was left out to keep people from whining about it being too realistic.
It wasn't entirely left out. Attacking the trainers is part of their A.I. Roulette for when you tell a Shadow Pokémon in Hyper Mode to use a non-shadow move. (So yeah, not something you're likely to see.)
In the first game, the first Shadow Pokémon you come across attacks Wes, knocking him back quite a bit. Rui then warns him that Shadow Pokémon will attack anything, including people.
About the Poké Ball thing, most of the people are given their Shadow Pokémon by Cipher, meaning Cipher probably gave them the Poké Ball it was contained in, and when you Snag them, it transfers them to a fresh one. It's totally possible that Team Cipher tampered with the Poké Balls to do as mentioned before.
The trainers you snag Pokémon from almost never seem to mind that you just stole their Pokémon. They get upset over being defeated and whine about that, but never once mention their now-stolen Pokémon or seem to care. Even if Wes or Rui or Michael took the time to explain to the trainer that there was something wrong with it off screen, it's hard to believe that the trainer would take that sitting down.
Well with Wes, can't explain. But in the second game, Michael is working with a big lab to do it, its possible they put out a message telling people someone would be snagging Shadow Pokémon and what happened. So perhaps that's why? Just a thought.
Wes is so unbelievably Badass that the Trainers he fights are left in awe, so they are unable to remember that Wes took their Pokémon at all.
How is even possible to take over the world with Shadow Pokémon? In both games, most can be beaten easily if you aren't trying to catch them.
They're infinitely less hesitant (that is to say, not at all) about attacking people, which would be fairly helpful when any retaliation is made by the populace.
They hit super effective against all types, so in theory the only reliable defense against a Shadow Pokémon is another Shadow Pokémon. You just beat them easily enough in game because they still aren't any better than the common trainers you always beat.
All I want to know is that why did Wes betray Team Snagem in the first place? They never show us any explanation on to why he would do something like that in the beginning. You join a gang of thieves, be their top soldier, and BOOM! You blow up their HQ and steal their prized weapon? The Hell?
He probably became disgusted with their actions, especially if he heard that they were cooperating with someone who could turn them into Shadow Pokémon.
Bulbapedia specifically states that Snagem was a small-time petty crime organization before Cipher came.
Bulbapedia is not a mouthpiece for the people who made the games, it isn't official, and since it didn't list where they got this from, we can't know for sure.
Bulbapedia is not a mouthpiece for the games, but the games themselves are—when you battle Gonzap for the first time in Colosseum, he reveals that before Cipher came along, Team Snagem were just petty thieves.
Rui doesn't let you snag non-Shadow Pokémon. Okay, it would make sense if Wes was a greedy and bad person, but what if you want to confisciate Pokemon from trainers, which abuse their Pokemon? Also wouldn't it be reasonable to snag Pokémon from Cipher, in order to prevent them becoming Shadow Pokémon in the first place?
When do Colo and XD take place anyways? Bonsly is refereed to as a new species in XD (5 years after Colo, DPPHGSS happen 3 years after RSEFRLG). Colo would need to happen before gen 3's other titles by at least two years. Are there any other implications of timelineness?
That's the big problem. Name a single instance in any non-Orre game where Orre is mentioned.
"Met in a distant land"? I meant more in the Orre games themselves.
Why does New York have species completely separate from Japan, but Arizona is littered with Japanese Pokémon?
Orre does not have any native Pokémon, and thus imports them from Hoenn and Kanto. There probably ARE a select few native Pokémon in the game, like the Cacturne-Expy, but then again, the Unova Pokémon didn't exist yet.
Doesn't explain the Poké Spots.
Although you can't get them until post-game, there are some older Pokémon in Unova, so... Poké-merica does have some Japanese Pokémon.
So why is it that pretty much every Shadow Pokémon you snag starts with a full shadow bar? I mean, if you're getting them from Cipher agents, sure, but do we assume that the random guys off the street never even bothered to take care of their Pokémon? Because really, that's all it takes to start reducing the bar.
Maybe they have some type of device that can refill the bar of a used Shadow Pokémon.
Or maybe they were starting to open up to their trainers when you nicked them. Notice how in Colosseum when battling them they use some of their non-shadow moves, which take a while to unlock when you're purifying them.
This is what I always thought. Along with the point right below this, it would also be a convenient answer for the people who complain that the Shadow Pokémon's old trainers can use non-shadow moves...
The shadow Pokémon might have to start all over when they get get a new trainer. To them, you're a stranger, and they can't trust you that easily.
Well every citizen with a Shadow Pokémon got it from Cipher, meaning that Cipher could have tampered with the Poke Ball to prevent a normal trainer from purifying them. When you Snag them, they're put in a fresh one without the tampering, letting you purify them. Just a theory.
Shadow Togepi; that pretty much serves as indubitable evidence that regardless of the Poké Ball, they're still Shadow Pokémon, and upon getting a new Trainer, they have to start all over in unlocking their hearts.
Orre is said to have no wild Pokémon in Colosseum. So, why are the markets selling Pokeballs at all? Sure, Team Snagem would buy them, but who else?
Based on the Outskirt Stand clerk's dialogue and fluff text elsewhere, I kind of get the impression that Orre had wild Pokémon a long time ago (but they all died out/were driven out), during which period they sold Poké Balls. By that logic, the initial batch from the Outskirt Stand is leftover stock from that period, and the clerk orders more later since he has a buyer for them.
The Outskirt Stand was the only location at which anyone could buy Poké Balls in Colosseum, and, even then, they claimed they hadn't had anyone to whom to sell them in quite a while.
Why is Michael so short? When playing a link cable match the trainers from other games are at least a head taller than him. Is he younger or is he just vertically impaired?
He's probably just really short. Note he looks shorter than quite a lot of the trainers in XD also. It was probably just done to emphasize that he's younger than Wes.
In Orre, there are healing machines freely available and simple enough for anyone to use. What is the point of having nurses (besides the ones outside the Pokémon Centers in Unova) in the rest of the Pokémon series if anyone can use the healing machines?
Save the trainer a bit of time, maybe? Or maybe Orre just doesn't have enough people to be nurses.
Considering the use of said healing machines is free, in every region so far, the question is why wouldn't you have a pretty nurse there to take a trainer's Pokémon and heal them with a smile? Since it's all probably paid for by local leagues. Orre being the odd one out, really has no need of nurses.
Why were Trudly and Folly taking Rui to Phenac City? Miror B.'s Hideout is in Pyritenote and Venus' hideout is accessed through an elevator in Miror B.'s hideout, and Ein's hideout is accessed through a train in Venus' hideout.
There IS a member of Cipher who has a hideout in Phenac. Evice. Notice that when you first reach Phenac, Bluno, Verde, Rosso, Nascour and Evice are all present. Presumably, one of them (likely one of the color trio) was supposed to collect Rui from Folly and Trudly and take her elsewhere (Ein's lab, if I had a guess). After all, they are NOT high enough rank to know where that is.
That occurred to me, but why would they take her directly to THE HEAD OF CIPHER'S hideout? Especially when said "hideout" is the house of the mayor of a city where two people dressed the way Trudly and Folly are, carrying a huge sack through town are a lot more likely to be questioned. If they weren't high enough ranked to know the location of the Shadow Pokémon Lab, they certainly wouldn't be a high enough rank to know that their leader was the mayor of Phenac.
So why the Shadow Remoraid that is more than 10 levels lower than the other Shadow Pokémon in the area?
The developers gave Reath a Remoraid to match Ferma's Mantine. Since Remoraid evolves at level 25 and Octillery doesn't have the association with Mantine that it's pre-evolution does, they couldn't make it level 30. Not the best explanation as Makuhita evolves at level 24 and is still caught at level 30, but it's the best I've got.
Practice keeping a low-level Pokémon in action, so you'll be ready when you get Plusle?