SPOILERS! Mysteries and Conspiracies of Pokemon

The Mewtwo Returns Special noted above is both the first encounter with Mewtwo that Ash & Co. are allowed to remember.

The original just kind of ended on the ambiguous departure. The special then reveals Mewtwo and the others were hiding out somewhere in Johto (Mew appeared, but I'm not sure if it was supposed to be real or just a vision by Mewtwo). The movie ends with Mewtwo letting the clones go off to live on their own, and the last shot is Mewtwo on a Roff-Spire overlooking a city.

Here's something I wonder about: Does the anime establish how Newtwo is able to Mega Evolve? I realize this was before X&Y were officially released, but Newtwo basically seems to be able to change forms at will, compared to actual evolution requiring both the Stone and some kind of connection to a trainer or human. Rayquaza is the only immediate exception I can think of, but I could explain the bond thing as being more a camaraderie or trust thing than outright friendship.

Newtwo is at best indifferent to humans, so that criteria's out the window. What if part of the experiments performed on it compared to the original Mewtwo was a way to force the Mega Evolution upon it?

The more I look into this though, the more it seems like this movie would have worked with the original Mewtwo instead. Ash at least knows him for the human half of the Mega Evolution, and being part of the form change would give them something to do besides sit around and pretend to be important by bonding with one of the Genesect.
Rayquaza isn't a huge exception, though. Yes, it has no need for any sort of Mega Stone, (just know a move you'd want on it anyway thanks to its diet of meteors that give off a similar energy) but it apparently can't Mega Evolve without receiving a 'fervent wish' to react to. It was the Draconids' prayers and wishes for salvation from disaster that allowed it to first Mega Evolve in ages past, and in-game whenever you're about to Mega Evolve it, the message, "(player's name)'s fervent wish has reached Rayquaza!" comes up. It still needs at least one human to go Mega. (even then that human needs a Key Stone to assist)
 
Mewtwo-two first mega-evolves in the special Prologue to Awakening, fighting the hunter Dirk's drones. And that's it, there's no special trigger or human emotional bond, or really any fanfare at all. It just kinda does it.

Best guess is that it's just a feature built into Mewtwo-two (as mentioned above).

Another thing about this Mewtwo I noticed going over this was it seems to have been hit with Ash's Pikachu level of power creep/power seep, in comparison to the original Mewtwo. While it still displays a lot of powerful psychic abilities, it just seems weaker than the original, and requires mega-evolving to be slightly effective, but only marginally. Granted, it's hard to put power levels on these things, combat effectiveness is difficult to rate.
 
Another thing about this Mewtwo I noticed going over this was it seems to have been hit with Ash's Pikachu level of power creep/power seep, in comparison to the original Mewtwo. While it still displays a lot of powerful psychic abilities, it just seems weaker than the original, and requires mega-evolving to be slightly effective, but only marginally. Granted, it's hard to put power levels on these things, combat effectiveness is difficult to rate.
Out-of-universe explanation:
Maybe it is a reference to how in the first generation, Mewtwo was hands down the most powerful Pokémon ever. Nowadays, it is simply a very, very powerful legendary, but not the strongest of them.
In-universe explanation:
What if Mewtwo-two is a clone of the original? The scientists who created her had a degraded sample of the original Mewtwo's DNA, resulting in less powerful version of it. Also, I've heard multiple times through science fiction that a clone of a clone is less viable, tends to be more sickly, etc., which is why after Jango Fett's death and some time had passed, the clone troopers were replaced with birth-born cadets in the Star Wars series. That could add to Mewtwo-two's apparent lack of strength compared to the original.
 
Out-of-universe explanation:
Maybe it is a reference to how in the first generation, Mewtwo was hands down the most powerful Pokémon ever. Nowadays, it is simply a very, very powerful legendary, but not the strongest of them.
In-universe explanation:
What if Mewtwo-two is a clone of the original? The scientists who created her had a degraded sample of the original Mewtwo's DNA, resulting in less powerful version of it. Also, I've heard multiple times through science fiction that a clone of a clone is less viable, tends to be more sickly, etc., which is why after Jango Fett's death and some time had passed, the clone troopers were replaced with birth-born cadets in the Star Wars series. That could add to Mewtwo-two's apparent lack of strength compared to the original.
Actually if the clone of a clone is done by embryo implantation it could become stronger or in the cases of rats develop a healthier defense system and live a bit longer.

However if an helix is reused from a damaged tissue for repeated process it could lead to failure on some functions in the long term.
 
Actually if the clone of a clone is done by embryo implantation it could become stronger or in the cases of rats develop a healthier defense system and live a bit longer.

However if an helix is reused from a damaged tissue for repeated process it could lead to failure on some functions in the long term.
Yes, but if you only use clone DNA without any additional "fresh" DNA, then it more than doubles the chance of genetic diseases being passed down. It's a little long winded to explain on this forum, so just read "What if?" by Randall Munroe (the XKCD guy) sometime.

But if Bulbapedia is to be believed, then Mewtwo-two was cloned directly from Mew DNA, just like the original Mewtwo.
 
New Mystery: Why exactly does Malva threaten to basically rip Looker's head off if he doesn't keep up his end of the bargain during the Looker side quest? What history is there between them?
 

Karxrida

Death to the Undying Savage
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New Mystery: Why exactly does Malva threaten to basically rip Looker's head off if he doesn't keep up his end of the bargain during the Looker side quest? What history is there between them?
I don't think there is a history between them. Malva did a plea bargain with him or something so she wouldn't get arrested for her involvement with Team Flare, and she was probably talking about that.
 

Pikachu315111

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How about this for mystery: exactly what did Looker have on Malva? It can be assumed it linked her to Team Flare, but what would it be? I mean I'd assume after the incident the authorities would have gone to the lab under Lysnadre's Cafe (at least the parts they knew about and could access) and got as much data from the computers down their as they could which would probably include a list of members (though that's assuming no one deleted the data which I'd imagine one of the admins would). I'd also assume Malva herself kept a low profile about being a member of Team Flare, being she's one of the Elite Four and news anchor. She didn't do anything directly with Team Flare but instead was probably just helping finance them and covering up their activities with false news stories. I guess maybe her financial records might have shown a connection, but then again her donations probably were going to Lysandre's foundation which I'm sure many people have donated and invested in so that would be a bogus trail. And it can't be the player since we only found out she was part of Team Flare after Looker made the plea bargain deal thus us not telling would be part of it. So all in all every visible path leads to a dead end so what did Looker have that was so incriminating that Malva agreed to the plea bargain (I'd imagine Malva would probably know what is solid evidence and what isn't).

Of course this is all assuming that's what her deal with Looker was about. We only assume that since its revealed to us Malva is part of Team Flare at that time, but that doesn't mean that's what the deal was. Looker had flimsy evidence that Malva was part of Team Flare but also had something else and that's what the deal was about. The flimsy evidence pointing Malva was part of Team Flare just let Looker know he could make a deal with her, but may not have been what the deal was about. So all this now turns to what was the deal Looker made with Malva. Maybe they'll bring it up again if they make a sequel to XY?

And to add onto what Karxrida said to this question:

New Mystery: Why exactly does Malva threaten to basically rip Looker's head off if he doesn't keep up his end of the bargain during the Looker side quest? What history is there between them?
Remember that Malva was very passionate about Team Flare's plan. She was ready to burn the player upon getting to her in the Pokemon League but kept her cool and realized that would be a bad move. Though her and Looker don't have a history just Looker being on the case and having found dirt on Team Flare (be it Malva being a member or something else) and she HAD to make a deal with him (a person who would have died if Team Flare's plan came into fruition) would be enough to get her ire. And though she said she didn't like Xerosic was experimenting on a child (killing them is okay, but experimenting on them? Perish the thought) she didn't really do anything to stop him (Malva was an admin so she could have probably ordered him to stop, at least doing the experiment with the child. Though he probably would have just took his stuff and left to continue with it anyway) showing she didn't really care either way so you can't use that as an excuse why she cooperated.

Though with all this said I do wonder what is Malva's story. Why is she so dedicated to Team Flare's plans? Like we can assume she probably though similarly to Lysandre, but what brought her to that way of thinking? Lysandre drove himself mad by wanting to help everyone but realizing he couldn't which lead him down a path where he created an apocalyptic future in his mind which he wanted to try and avert. However Malva doesn't seem like the type, she seems like the type would just wanted to purge the world of people she considered lesser than herself but why?
 
Speaking of Malva, she happens to have a really funny line in that sidequest:

"Took you long enough, <player>. It may happen that I have need of your services, but I expect you to keep in mind how valuable my time is! Oh, never mind! Just fight me! I can't possibly have a reasonable discussion when my emotions are so inflamed!"

And then there's this:

"If you want to help the girl, you need to put a stop to Xerosic. And that I can help you with! If we leave now, we should find him at Lysandre Café. Don't dawdle. Be ready to face death if you go. Prepare well if you want a shot at surviving."

Um...so did the localization team miss that one or something? Why is there a blatant mention that you might die (even though we all know you won't) in a Pokemon game? That's a mystery to me.
 

Pikachu315111

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If I recall correctly, Malva tells the player, at the hotel, that she was the queen of Team Flare. Which would be supported by her female Pyroar. The fact that she's a famous person in Kalos would help gain support for their particular cause.
She never says that, she actually never says what her position in Team Flare was besides she was in it. Many assume she was at least an Admin not only because she's a member of the Elite Four and a popular anchor woman but also because when she gave you access to the secret floor she says its a floor only admins knew about. Though even if she said she was queen, what does her being "queen" mean? What's her role as queen?

Speaking of Malva, she happens to have a really funny line in that sidequest:

"Took you long enough, <player>. It may happen that I have need of your services, but I expect you to keep in mind how valuable my time is! Oh, never mind! Just fight me! I can't possibly have a reasonable discussion when my emotions are so inflamed!"

And then there's this:

"If you want to help the girl, you need to put a stop to Xerosic. And that I can help you with! If we leave now, we should find him at Lysandre Café. Don't dawdle. Be ready to face death if you go. Prepare well if you want a shot at surviving."

Um...so did the localization team miss that one or something? Why is there a blatant mention that you might die (even though we all know you won't) in a Pokemon game? That's a mystery to me.
Could be Malva trying to drum up some drama and suspense to intimidate you. She's maybe "helping" you but she still sees you as an enemy so is either trying to mess with you or make it sound like Team Flare is still a threat. Of course considering the power that Essentia has and with her under control of Xerosic who shows no problem using a child for his experiments she could be telling you that the situation could get deadly dangerous fast if Xerosic just sends Essentia right at you (she took Looker down in one punch that at the very least he considered needing to go to the hospital).
 
"If you want to help the girl, you need to put a stop to Xerosic. And that I can help you with! If we leave now, we should find him at Lysandre Café. Don't dawdle. Be ready to face death if you go. Prepare well if you want a shot at surviving."

Um...so did the localization team miss that one or something? Why is there a blatant mention that you might die (even though we all know you won't) in a Pokemon game? That's a mystery to me.
Yeah, I found that odd when I was doing the Looker side quest today, and actually had to go talk to her again just to make sure I read that right.
 
She didn't do anything directly with Team Flare but instead was probably just helping finance them and covering up their activities with false news stories. I guess maybe her financial records might have shown a connection, but then again her donations probably were going to Lysandre's foundation which I'm sure many people have donated and invested in so that would be a bogus trail. And it can't be the player since we only found out she was part of Team Flare after Looker made the plea bargain deal thus us not telling would be part of it. So all in all every visible path leads to a dead end so what did Looker have that was so incriminating that Malva agreed to the plea bargain (I'd imagine Malva would probably know what is solid evidence and what isn't).

Of course this is all assuming that's what her deal with Looker was about. We only assume that since its revealed to us Malva is part of Team Flare at that time, but that doesn't mean that's what the deal was. Looker had flimsy evidence that Malva was part of Team Flare but also had something else and that's what the deal was about. The flimsy evidence pointing Malva was part of Team Flare just let Looker know he could make a deal with her, but may not have been what the deal was about. So all this now turns to what was the deal Looker made with Malva. Maybe they'll bring it up again if they make a sequel to XY?
That's more your interpretation of the events than what was explicitly revealed. All the game told us is: 1. Malva was in Team Flare, 2. Looker knows that she is connected to Team Flare. The how's and why's are opinion.

Plus the money trail ain't such a loose end. Remember that to join Team Flare, you're required to donate 5,000,000 Pokedollars, painting a gigantic target of suspicion on everyone who donated over that amount. We know Malva was a member of some rank, so she had to have donated the red-flag amount of five million.

Plus considering how real governments react to terrorist plots, I wouldn't be surprised if threatening to destroy the world caused a global witch-hunt for anyone with even the remotest or flimsiest connection to Team Flare. They did try to obliterate all life on the planet after all, that tends to cause an extreme reaction.

Heck, Malva probably went to the authorities herself and admitted to everything in exchange for amnesty and secrets, just so she would have the agency in her decision and look more remorseful in presentation, rather than wait for the cops to bang on her door.

Edit: The witch hunt idea gave me another theory on Looker's dirt on Malva, if the public ever knew she was a Team Flare member (or even just suspected of associating with them) it would essentially be a career-killer for her even if she faces no legal repercussions for it. Can't have your news journalist donating to terrorists, right?
 
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To be fair, it ain't THAT hard for Looker to think about investigating Malva. The leader of Team Flare is also the same guy that gives Malva her paychecks as a reporter for the Holo Caster. It's not TOO much to suspect her of something; Malva has strong connections with Lysandre. In real life, the first people you start suspecting of being in the mob are the friends of the people you know ARE in the mob. So, just a little snooping for this international detective would give him enough evidence to figure out Malva was a high-level Team Flare agent.
 

Pikachu315111

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To be fair, it ain't THAT hard for Looker to think about investigating Malva. The leader of Team Flare is also the same guy that gives Malva her paychecks as a reporter for the Holo Caster. It's not TOO much to suspect her of something; Malva has strong connections with Lysandre. In real life, the first people you start suspecting of being in the mob are the friends of the people you know ARE in the mob. So, just a little snooping for this international detective would give him enough evidence to figure out Malva was a high-level Team Flare agent.
Oh yeah, I totally forgot that Malva worked for Lysandre on the books, lol. Well then I guess that would automatically put you on the list of suspects.

That's more your interpretation of the events than what was explicitly revealed. All the game told us is: 1. Malva was in Team Flare, 2. Looker knows that she is connected to Team Flare. The how's and why's are opinion.

Plus the money trail ain't such a loose end. Remember that to join Team Flare, you're required to donate 5,000,000 Pokedollars, painting a gigantic target of suspicion on everyone who donated over that amount. We know Malva was a member of some rank, so she had to have donated the red-flag amount of five million.

Plus considering how real governments react to terrorist plots, I wouldn't be surprised if threatening to destroy the world caused a global witch-hunt for anyone with even the remotest or flimsiest connection to Team Flare. They did try to obliterate all life on the planet after all, that tends to cause an extreme reaction.

Heck, Malva probably went to the authorities herself and admitted to everything in exchange for amnesty and secrets, just so she would have the agency in her decision and look more remorseful in presentation, rather than wait for the cops to bang on her door.

Edit: The witch hunt idea gave me another theory on Looker's dirt on Malva, if the public ever knew she was a Team Flare member (or even just suspected of associating with them) it would essentially be a career-killer for her even if she faces no legal repercussions for it. Can't have your news journalist donating to terrorists, right?
True, but what if Malva donated more being she would have lots of money and was dedicated to the cause? I'm sure there are plenty of businesses and entrepreneurs who had donated and invested into Team Flare well over 5 million. While sure they can suspect all of them being members of Team Flare I doubt that all of them are.

But the criminals would still need to go through the justice system. You can go on a witch hunt and declare thousands of people a member but if there's no evidence to prove them guilty it's a waste of time. The officials would just have to follow logical trails to possible suspects which, while Malva would be on the list as explained, would have lack of proof to support her.

I guess Malva could have done that, meaning whatever deal her and Looker made wan't her secret of membership. But the way that they acted didn't seem that was the case. If that was the case why was Looker so opposed to making a deal with Malva? He would know if she turned herself in meaning asking for her assistance would be a tool instead of a last resort which was how it was presented.

And her career and possibly even life being ruined by being revealed to be part of Team Flare is obviously why she'd want to hide it. I don't think there was ever a question why she wanted it to be kept secret from the public.

And here's another thought: if a member of the Elite Four was a member, who's to say other official members weren't? What if someone who had power to choose who did the investigations was part of Team Flare, assigned themselves to the job, and did what he could to protect as many members as possible? Or what if members of the investigation team were Team Flare members and hid evidence from the officials? How deep does this rabbit hole go?
 
I guess Malva could have done that, meaning whatever deal her and Looker made wan't her secret of membership. But the way that they acted didn't seem that was the case. If that was the case why was Looker so opposed to making a deal with Malva? He would know if she turned herself in meaning asking for her assistance would be a tool instead of a last resort which was how it was presented.

And her career and possibly even life being ruined by being revealed to be part of Team Flare is obviously why she'd want to hide it. I don't think there was ever a question why she wanted it to be kept secret from the public.
I meant more that media sensationalism as a career-killer for Malva, whether the accusation was true or not (just watch tumblr go wild on completely false rumors, it's not that hard to start a riot from a lie).

So in my theory:

Malva, seeing Team Flare going down, does the sensible thing and turn herself in, exonerating herself with a plea-bargain.

Looker, worried about his missing sorta-adopted-daughter of 3 days (yeah, not much sense there, but it's my wacky fan-theory), threatens Malva to go back on their deal by outing her Team Flare involvement to the public, which could ruin her career even if the rumors are denied by herself or the police (being completely true is just the cherry on top). He's initially reluctant due to this cowboy-cop tactic being on the gray side of unethical, but worry for Emma prevails.

Malva relents, and gives up even more classified details about Xerosic, but stubbornly with much outward resentment that gets directed at the player when you confront her.

Completely from my head and with little game support? You betcha'! But it reads more like a detective novel and (in my head) explains why Looker gives up the Kalos detective branch and leaves so easily in the end (guilt of resorting to unethical behavior to solve a mystery).

But as pointed out a while ago, Pokemon law enforcement makes no sense. Archie, Maxie, Malva, and many more would be jailed flat for their crimes (ecoterrorism and working with a known criminal organization/funding terrorism) but despite facing certain doom, the boy in the pokemon center just cares about his shorts and his rattata.

I digress.

In other news, it looks increasingly certain that the new green snakey thing is related to Zygarde, based on the latest Corocoro and Mega Evolution special trailer. Specially since you get a look at their backside, where they have a hexagon pattern.
 

Pikachu315111

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I meant more that media sensationalism as a career-killer for Malva, whether the accusation was true or not (just watch tumblr go wild on completely false rumors, it's not that hard to start a riot from a lie).

So in my theory:

Malva, seeing Team Flare going down, does the sensible thing and turn herself in, exonerating herself with a plea-bargain.

Looker, worried about his missing sorta-adopted-daughter of 3 days (yeah, not much sense there, but it's my wacky fan-theory), threatens Malva to go back on their deal by outing her Team Flare involvement to the public, which could ruin her career even if the rumors are denied by herself or the police (being completely true is just the cherry on top). He's initially reluctant due to this cowboy-cop tactic being on the gray side of unethical, but worry for Emma prevails.

Malva relents, and gives up even more classified details about Xerosic, but stubbornly with much outward resentment that gets directed at the player when you confront her.

Completely from my head and with little game support? You betcha'! But it reads more like a detective novel and (in my head) explains why Looker gives up the Kalos detective branch and leaves so easily in the end (guilt of resorting to unethical behavior to solve a mystery).

But as pointed out a while ago, Pokemon law enforcement makes no sense. Archie, Maxie, Malva, and many more would be jailed flat for their crimes (ecoterrorism and working with a known criminal organization/funding terrorism) but despite facing certain doom, the boy in the pokemon center just cares about his shorts and his rattata.

I digress.

In other news, it looks increasingly certain that the new green snakey thing is related to Zygarde, based on the latest Corocoro and Mega Evolution special trailer. Specially since you get a look at their backside, where they have a hexagon pattern.
Sounds like an alright theory now fully laid out. Still if Malva has submitted herself to the police then not only should Looker have a problem asking her for assistance but wouldn't even need to make a deal with her. She'd already be working with the police which means she would have to tell everything she knew.

Also its sorta implied Emma has been living with Looker for weeks as he taught her how to read and write though sadly the way the Looker Mission was done it seemed like it was only a few days. It felt like they wanted to do the Looker Missions throughout the game, like every time you naturally went back to Lumiose City, but probably knowing they needed post game content decided to stick it all at the end.

Also Looker was there for Xerosic in the first place, the Detective Agency was just a front. Once he got Xerosic he was going to leave no matter what.

And yes, criminal justice in the Pokemon world is a joke. I'd like to think at the very least the Pokemon League is keeping an eye on the former syndicate teams. Like in DPP Saturn isn't in hiding and ORAS changed it so neither was Archie/Maxie and their admins. Heck in BW2 they showed that Rood, Anthea, Concordia, and other former Plasma grunts were actively working in Driftveil to make amends for what they done (probably under the authority of Clay).
 
Couldn't find it in the archive so I will just ask this here:
Has it ever been explained what Pokerus is (I think the Nurse commented on it being a Bacteria but that's all I remember) and how they show properties like Doubling EVs gained, spreading around on active Pokemon and not expiring in PCs? And what caused the Pokerus to expire anyway?
 
Couldn't find it in the archive so I will just ask this here:
Has it ever been explained what Pokerus is (I think the Nurse commented on it being a Bacteria but that's all I remember) and how they show properties like Doubling EVs gained, spreading around on active Pokemon and not expiring in PCs? And what caused the Pokerus to expire anyway?
As far as in-game story behind it, no.
 
Couldn't find it in the archive so I will just ask this here:
Has it ever been explained what Pokerus is (I think the Nurse commented on it being a Bacteria but that's all I remember) and how they show properties like Doubling EVs gained, spreading around on active Pokemon and not expiring in PCs? And what caused the Pokerus to expire anyway?
As for what it is, it seems to work like a common virus- it comes, infects everyone quickly, then goes away. Except pokerus makes you stronger( well, makes it easier for you to become stronger), whereas common viruses weaken you( for their duration at the very least). I'm not sure about why it affects EVs though, I'm interested to see if anyone has some theories on that.
 

Pikachu315111

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Couldn't find it in the archive so I will just ask this here:
Has it ever been explained what Pokerus is (I think the Nurse commented on it being a Bacteria but that's all I remember) and how they show properties like Doubling EVs gained, spreading around on active Pokemon and not expiring in PCs? And what caused the Pokerus to expire anyway?
Here is what the Pokemon Center Nurse and Professor Elm say:

Pokemon Nurse:
Oh... It looks like your Pokemon may be infected with the Pokerus.
Little is known about the Pokerus, except that it is a microscopic life-form that attaches to Pokemon.
While infected, Pokemon are said to grow exceptionally well.

Professor Elm (calling player after Pokemon catches Pokerus in HGSS):
"Hello, (player)?
I discovered an odd thing.
Apparently there's something called Pokerus that infects Pokemon.
Yes, it's like a virus, so it's called Pokerus.
It multiplies fast and infects other Pokemon too. But that's all.
It doesn't seem to do anything, and it goes away over time.
I guess it's nothing to worry about. Bye!"

Professor Elm (player calls him in HGSS):
Hello, (player)?
It seems that Pokemon that have been infected with Pokerus level up better.
We're not quite sure why..."
How did Elm become a professor...

Anyway, we won't get into the misconceptions with those statements (like viruses aren't life forms since they can't reproduce without a host (who's cells it infects and essentially destroy to make more of itself) and thus viruses are parasitic so not good for the host cells) though we will need to sort of split up this conversation in two because there's a difference from what a virus is which is where Pokerus gets its name and what a bacteria/archaea/eukaryote is which is what the description makes it sound like.

If we're to assume its actually a virus then we'll focus on a virus' infecting and reproduction method. Though I said viruses were not good for the host that's not technically a bad thing depending on what the cells its preying on. Viruses have preferred prey and if they prey upon bacteria that causes diseases then they'll obviously be good for the host who gets sick from said diseases. So with that said the Pokerus is a beneficial virus so it must get rid of something that prevents a Pokemon from usually getting double EVs. If I had to make something up I'd say maybe Pokerus prey on weak or sick cells and destroys them, thus any of the experience energy those cells would normally absorb (and waste since they wouldn't properly be able to use them) would be absorbed by other healthy cells and especially the newer healthy cells the body made to replace the destroyed cell. Thus the EV the Pokemon is getting is because its getting the benefit of ALL the experience energy it has earned instead of losing some of it due to weak and sickly cells. Of course since there's only so many weak and sickly cells in one body, once there's no more the virus dies out as it has no means to reproduce. Also with it unable to reproduce the Pokemon's immune system is able to fully recognize the virus and get to work cleansing it from the body (it may be beneficial but its still a foreign element in the body to the white blood cells). As an extra precaution the body could have made the new healthy cells be immune to the Pokerus though that comes with the beneficial side effect of the double EVs becoming permanent as those cells are less likely to get weak and sick. But still that means the Pokemon can't catch Pokerus again.

If we're to assume its actually a microscopic life form like a bacteria/archaea/eukaryote, we can assume the relationship between it and host is mutualistic. For allowing it to live within the Pokemon and take in some of the experience energy it possibly releases an enzyme that causes a chemical reaction which results in double EVs. And since its replicating its creating more of itself thus when they feed on experience energy the more enzyme is being released. But at some point the guest starts turning into an invader as the more and more of it is created thus might as some point be taking in more experience energy then the body would allow it too. Its time for the immune system to do its thing and send out white blood cells to get rid of them and now that it fully recognizes it won't allow any more Pokerus. Its also possible the very enzyme they released makes the host now less inhabitable by any other Pokerus (but since the enzyme still exists in the hosts system its still strengthening the Pokemon and giving it double EVs).

So pick whichever the one you think sounds right. OR, we could maybe assume the Pokerus is a completely new life form that maybe takes on both a characteristic of a microscopic life form and a virus. Like it can replicate on its own but takes longer than other microscopic life forms to do, so it has also learned to infect weak and sick cells to reproduce more of itself that way. While initially let be by the body as its producing that beneficial enzyme, once it starts destroying cells (even though their weak and sickly), the body's immune system activates and white blood cells are sent out to deal with the "threat". So its both releasing a beneficial enzyme and getting rid of weak/sickly cells while the immune system works to wipe it out and makes the Pokemon immune to it.

As for why does Pokerus not expire in the PC or Daycare? Well for the PC I've personally always say it that the Pokemon is put into suspended animation, so all its bodily functions also stop including the immune system (though this also means the Pokerus has been suspended so it needs neither to reproduce/replicate or worry about dieing out). The Daycare is a bit more tricky though with all the Pokemon around it could just be that is a huge neverending breeding ground as Pokemon are spreading their Pokerus to each other and the immune system can't get a read on what its dealing with (at least until taken out of the Daycare).
 
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Perhaps pokerus is a normal virus (in most ways comparable to a human common cold), with the normal effects of a virus, but it happens to release a chemical in the process of invading and taking over cells that makes the pokemon gain EVs more effectively. If the virus is weak enough that the immune system can fight it in a few days, that would match what we see.
 
I always theoried that Pokerus was a viral form of Deoxys, just without the cosmic radiation that mutated it into the pokemon we know.

Don't have anything in-game to suggest that though, but I always thought that Deoxys' form changing based on primary stats (attack, defense, and speed form) was related to effort values.
 
Uh, super necrobump for another ghost post...
I know we've already gone over a couple of ghostly gals, but in Phoebe's room in OR AS, there is a ghost child that appears right when the challenge screen comes up. It's on the armchair behind her to her right. After the battle, when the camera is facing your right shoulder, the ghost can be seen behind your left side.

Why is it there? Does Phoebe have some ghosts in her past? Or did she summon it using some paranormal power to mess with your mind? According to bulbapedia, the ghost child's gender is the opposite of yours...

(Sorry if we discussed this and I missed it)
 
Just the designers appealing to their demographic, kids love ghost stories in Japan... A lot.

Apparently the whole haunted Manor/villa in Sinnoh and B2W2 Unova was really popular among them so they just catered towards it.

Don't think too much about it, there seems to be a lack of special things tied around them as proved by the XY ghost datamine, it's just that a couple of Edge fankids starving for "maturity" to validate themselves liking what's perceived as a kids game just put these kind of content through memetic status on the Internet.
 

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