SPOILERS! Mysteries and Conspiracies of Pokemon

Pikachu315111

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Right, that means I not only have to KNOW what every battle will yield, but keep track of them too. What a PITFA!
What do you mean? Every Pokemon of the same species gives out the same EV yield. Remember, Bulbapedia is your friend:

Horde Encounters
EV Yields

Just figure out which EV you want to increase, and use the above two lists to figure out which Pokemon to focus on. You could also follow these guides:
XY Horde EV Training
ORAS Horde EV Training
 
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brightobject

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Yeah, if you don't know anything and you're not without internet, the 'I can't remember all this info' thing doesn't work as an excuse anymore. Not only bulbapedia but the entire Internet is your friend.
 
Not to be a nag, but half a page discussing EV mechanics are not a mystery. Take it to the Unpopular Opinions page or let it drop.

For a transition: Shadow Pokemon. While so critical to the plots of Colosseum and XD, we never got an answer about how they are created. Our best answer was that science people did science stuff to create a science machine for science, science. Even when we got to the lab that created Shadow Pokemon, there was a distinct lack of answers in this department.

We know a lot about the effects: lack of empathy, unique eldritch attacks, rage issues.

And we know a lot about the cure: Deus Ex Celebi or lots of what can only be described as Poke-therapy (one-on-one, group therapy, herbal, etc.) followed by a seance ritual.

So given the new stuff that's come out since Gen3 (particularly mega evolution and infinite energy), do we have any theories about what seals a Shadow Pokemon's heart?
 

Celever

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Not to be a nag, but half a page discussing EV mechanics are not a mystery. Take it to the Unpopular Opinions page or let it drop.

For a transition: Shadow Pokemon. While so critical to the plots of Colosseum and XD, we never got an answer about how they are created. Our best answer was that science people did science stuff to create a science machine for science, science. Even when we got to the lab that created Shadow Pokemon, there was a distinct lack of answers in this department.

We know a lot about the effects: lack of empathy, unique eldritch attacks, rage issues.

And we know a lot about the cure: Deus Ex Celebi or lots of what can only be described as Poke-therapy (one-on-one, group therapy, herbal, etc.) followed by a seance ritual.

So given the new stuff that's come out since Gen3 (particularly mega evolution and infinite energy), do we have any theories about what seals a Shadow Pokemon's heart?
The biggest clue to how Shadow Pokemon are created is in the Shadow Pokemon Lab. As the name suggests, it's literally a lab to create Shadow Pokemon. How does it do so? As cruel as it sounds, it's highly hinted at that the DNA of the Pokemon is modified through some kinds of cruel means, because of the way you open the door to Cipher Admin Ein -- finding 3 DNA Samples from Shadow Pokemon previously encountered in the game. The subway from The Under to the Shadow Pokemon Lab also has cages which it's explicitly stated transported Shadow Pokemon. The reason why Celebi is the Pokemon to cure the Shadow Pokemon, besides it being a way to actually catch the Pokemon (if you're Japanese), is that it reverts the Shadow Pokemon, or at least its mental state, to a time before it was experimented on.
 
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Pikachu315111

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For a transition: Shadow Pokemon. While so critical to the plots of Colosseum and XD, we never got an answer about how they are created. Our best answer was that science people did science stuff to create a science machine for science, science. Even when we got to the lab that created Shadow Pokemon, there was a distinct lack of answers in this department.

We know a lot about the effects: lack of empathy, unique eldritch attacks, rage issues.

And we know a lot about the cure: Deus Ex Celebi or lots of what can only be described as Poke-therapy (one-on-one, group therapy, herbal, etc.) followed by a seance ritual.

So given the new stuff that's come out since Gen3 (particularly mega evolution and infinite energy), do we have any theories about what seals a Shadow Pokemon's heart?
Another thing to note about Shadow Pokemon is that they specifically talk about ARTIFICIALLY closing a Pokemon's Heart. This hints that a Pokemon is capable of closing its heart in some way, maybe as some kind of defense mechanism, and what Cipher is doing must be beyond putting the Pokemon in a situation it'll naturally close its heart. My guess this has to do with keeping the Shadow Pokemon permanently as a Shadow Pokemon since if a Pokemon can naturally close its heart it can open it back up naturally as well. Thus Cipher would have to do something to bypass the natural mechanism that triggers the closing of the heart and prevent the trigger from it opening on its own (at least without a trainer's help).

As Celever said, some genetic manipulation sounds like a likely case. If not affecting the DNA itself then using chemicals to alter the Pokemon's state of being almost permanently. They could probably also do physical and mental torture as well, but I imagine them only doing so to weaken the Pokemon enough that the experiments to artificially close its heart works.
 

brightobject

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I'm pretty sure it's not just a 'natural state' given permanence though, they're obviously introducing foreign elements into a Pokemon's biology given their new shadowy auras/etc. I can imagine some contrived 'Chemical X' sort of thing being involved that modifies their genes in some fashion? (as mentioned before), perhaps similar to the virus Solanum from World War Z, given that said process (es) obviously completely repurpose a Pokemon's biology
 
The whole "closed heart" thing is like an affectation of the first Dark Pokemon cards in the tcg. The Pokemon become Dark Pokemon because of the ill-natured way they were brought up.

Something I thought about creating Dark/shadow Pokemon by scientific means: there's a scientific study developing principles of "quantum harmonics", which uses these long,meditative soundtracks in conjecture with a chair that blasts different segments of your body with powerful sound waves that act like a massage therapy. They have an entire session using this practice that can help open and balance your chakras. So, maybe there's a practice of sorts that alters a given Pokemon's psyche to become a Dark Pokemon that compresses the need for having a malevolent trainer into a type of digitized abuse-session.

This also kind of ties into the mysteries of Delta Species Pokemon. They say that the scientists of the Holon region were experimenting with a type of radiation that caused the local wild Pokemon to mutate into new attributes. The scientists of this universe can do all kinds of stuff. In a weird way, I think it makes sense that, if they can create TMs to edit your Pokemon's novelist artificially, there's nothing stopping them from making new technology that can edit stats more personal to a given species.
 

Pikachu315111

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I'm pretty sure it's not just a 'natural state' given permanence though, they're obviously introducing foreign elements into a Pokemon's biology given their new shadowy auras/etc. I can imagine some contrived 'Chemical X' sort of thing being involved that modifies their genes in some fashion? (as mentioned before), perhaps similar to the virus Solanum from World War Z, given that said process (es) obviously completely repurpose a Pokemon's biology
When I was talking about a "Shadow Pokemon" being a natural state they can go into I was thinking along the lines of a person suddenly pumping themselves with adrenaline (a fight or flight response). Like say a person backs a Pokemon into a corner and that person plans on killing that Pokemon. Normally a Pokemon won't attack a human, Pokemon seem to have a mental block that makes attacking a human taboo. But that Pokemon is going to die if it doesn't do something, so what if its able to close its heart? Suddenly that mental block is gone and the Pokemon can now attack the human and run off; it may feel bad later for doing it but it would have been a natural response so it couldn't have stopped it.

And just thinking about it, maybe a Pokemon closing its heart is a way for the Pokemon to actually further protect itself from permanent damage? Maybe the Cipher scientists misunderstood what was going on when their experiments to close a Pokemon's heart was successful. What if instead of that being the natural result its instead the Pokemon's body responding to the torture/corruption and closes to prevent further damage to the Pokemon's heart/soul/mind. Doing so has the Pokemon enter a vicious state but under the care of a kind trainer the heart can slowly reopen as the damages done are healed and the lingering corruption is purged. Heck, maybe that's what Lovrina figured out what was happening in XD and using that knowledge attempted to make XD001 unpurifyable by either preventing the heart from being opened or "getting through" the heart closing and corrupting the heart/soul/mind (which could explain its change in appearance).
 

brightobject

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No, I'm saying whatever they do alters the Pokemon at a fundamental level, because when in Shadow form they do things impossible for them when they aren't Shadow Pokemon. QED. So comparing Shadow powers to Pokemon's natural abilities is shaky at best (e.g. the best you could do is say that Shadow Pokemon's abilities are a warping and amplification of tendencies already included in Pokemon as part of their natural makeup, but that doesn't make any sense because certain parts of Shadow-ification are constant across all species, such as the fiery aura).
 

Pikachu315111

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No, I'm saying whatever they do alters the Pokemon at a fundamental level, because when in Shadow form they do things impossible for them when they aren't Shadow Pokemon. QED. So comparing Shadow powers to Pokemon's natural abilities is shaky at best (e.g. the best you could do is say that Shadow Pokemon's abilities are a warping and amplification of tendencies already included in Pokemon as part of their natural makeup, but that doesn't make any sense because certain parts of Shadow-ification are constant across all species, such as the fiery aura).
What does a Shadow Pokemon that was forced to close its heart do that would be impossible for a theorized Pokemon who can naturally become a Shadow Pokemon under extreme conditions? When a Pokemon closes its heart it gains the Ability of a Shadow Pokemon, simple as that.
 

brightobject

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What does a Shadow Pokemon that was forced to close its heart do that would be impossible for a theorized Pokemon who can naturally become a Shadow Pokemon under extreme conditions? When a Pokemon closes its heart it gains the Ability of a Shadow Pokemon, simple as that.
It's not natural for Pokemon to become Shadow Pokemon.
 

Pikachu315111

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It's not natural for Pokemon to become Shadow Pokemon.
I know that, what I'm saying is that it's possible maybe under extreme circumstance a Pokemon may close its heart in order to do things it normally couldn't do. Sort of like how a human would pump adrenaline through their body.
 

Celever

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I must say, Pikachu315111, I don't actually think that the use of "artificially" closing their heart implies that it can be done naturally. From my research I think that Pokemon Colosseum was released at a time where there was a lot of "terror" surrounding modification of DNA and artificial things in general. It could well have just been a buzzword the developers threw in to make Cipher seem even more evil. A piece of evidence supporting this theory is the fact that the whole artificial thing sort of dies out in Pokemon XD: Gales of Darkness and is mentioned very rarely if at all in the game -- I can't recall a single example.

It's a nice idea, though, and I can see it being an interesting twist on the story. I guess the best analogy would be honeybees; if put in a state where they feel in danger they kill themselves to try and stop the attackers from killing more of their hive by stinging them. This theory of Shadow Pokemon naturally closing their hearts in times of need to possibly protect their trainers is something which could have been in the games, but it just plain isn't.
 
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Pikachu315111

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I must say, Pikachu315111, I don't actually think that the use of "artificially" closing their heart actually implies that it can be done naturally. From my research I think that Pokemon Colosseum was released at a time where there was a lot of "terror" surrounding modification of DNA and artificial things in general. It could well have just been a buzzword the developers threw in to make Cipher seem even more evil. A piece of evidence supporting this theory is the fact that the whole artificial thing sort of dies out in Pokemon XD: Gales of Darkness and is mentioned very rarely if at all in the game -- I can't recall a single example.

It's a nice idea, though, and I can see it being an interesting twist on the story. I guess the best analogy would be honeybees; if put in a state where they feel in danger they kill themselves to try and stop the attackers from killing more of their hive by stinging them. This theory of Shadow Pokemon naturally closing their hearts in times of need to possibly protect their trainers is something which could have been in the games, but it just plain isn't.
Well I was just trying to come up with an explanation to how Cipher was able to make Shadow Pokemon by making it them manipulating a not often use defense mechanism within the Pokemon's biology. Because otherwise the answer would probably be they exposed them to "evil rays" or something (since I don't think normal physical or mental torture would create a Shadow Pokemon as the ones Cipher wants).

I think we should end it on the note that no matter how they do it, it doesn't matter. The point is Cipher has found a way to make a Pokemon who's willing to attack people by closing their hearts and they need to be stopped. The good guys have developed a way to reverse it so they don't need to know, nor would they probably want to.
 
Guys... have you seriously tried Chinese herbal medicine before?
It's so freakingly bitter that nothing compares, and everyone gladly takes the flavored Western medicines.
(in the Japanese games, those herbal medicine are said to be Chinese medicine, but the dubs censored it)

I think the bitter poke blocks are slightly bitter, like coffee or matcha, that makes certain people and pokemon like them.
So that some Pokemon love them.

But herbal medicine is like omfg wtf type of bitter that no one likes.

A lot of people I know love matcha, but I don't know anyone who likes the taste of Chinese medicine.
It depends, right? I'm incredibly used to bitter stuff. To me, some bitter stuff doesnt even taste bitter anymore, I luuuuuuuurve the taste of chinese ginseng (it actually tastes sweet to me...) Some stuff will do me in though, if it's bitter and has a weird taste (bitter with a chivey taste is my pet hate) them urk. BUT on the Pokemon thing; animals get used to it. Our cats have had plenty of bitter herbs/nutrients/foods (cat safe ones) that they've simply gotten used to. Bodies have a way of "adapting/changing" how your taste buds percieve certain foods after eating something many times if your body realises it's getting "the god stuff" from it. As for those types that enjoy bitter foods; they SHOULD rectify this and let those Mon use those items hassle free, heck maybe even GIVE friendship value to them?

Bitter Medicine: In FRLG the descriptions for the Herbal Medicines have changed from saying "a bitter powder" to "a very bitter medicine powder" (except in the Colosseum games) and kept that way since. While that could be explained with items begin given a bigger description space, it could also be the designers realized it doesn't make sense Pokemon who like bitter to not like it so they emphasized its "very" bitter compared to probably the more modest bitter flavors of Pokeblocks and Poffins.

Edible Revives: I always just saw Revives as just hard vitamins. They never really looked like a capsule to me (and even if the were I would assume it would be a consumable capsule).
I like to think of revives as some sort of crushable-to-powder crystal that is infused with life energy/force, possibly growing in some deep cavern somewhere where they're mined, but can also be artificially grown. Bright described it like I saw it. It can be eaten, inhaled, absorbed through skin.

On shadow Pokemon. Damn I'd like to see them again. Maybe a post-game episode in Z where Wes comes to town and you help him hunt some lost ones down? As for the "shadow" it's all to do with energy, EVERYTHING is to do with energy in Pokemon. The one thing about Mon is; their energy is very malleable. It's like the energy has only just taken on the form of matter and is unstable/in a state of flux somehow. Evolution, parasitc bonds, mega evolution, radiation/energy from stones being absorbed/altering them, emotional energy adjustments to itself etc. I had a post ready about it (it can wait), but my theory on this shadow is the shadow part is something that's been done to them, something negative, likely torture. I think love energy naturally flows from a Mon's heart, and that a Mon would quickly undo the "shadow" effect done to them except their heart has been artificially closed/locked shut so it can't naturally heal. A heart has to be artificially shut/closed FIRST for the shadow effect to start to take hold (shadow effect likely grows from negative experiences) otherwise the love energy from a Pokemon's heart will simply naturally/continously heal the negative effects to stop it ever becoming FULL shadow.

MOD EDIT: Don't double post. Use the Edit button.
 
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The idea behind Shadow Pokemon may have been like a "forbidden power" thing. there are numerous other shows that feature some kind of superpower that few can master without being consumed by it. The Cipher scientists created a new type (Shadow) that has an upper hand against all naturally-occurring types. They intended on making it a secret weapon to use Pokemon with a catch-all technique to defeat their opponents quicker and advance their hostile-takeover bit. But since regular Pokemon can't learn Shadow moves, they needed to have Pokemon in a state that would allow for use of this new technique.

So, the scientists may have concluded that forcing the Shadow type onto Pokemon would have been more efficient/cost effective than gene-splicing to create their own new Pokemon. In doing so, the access they get to Shadow moves comes at the cost of their ability to surpass their current experience level (their heart has been closed to the chance of growing beyond their experiences up to the point of being turned into a Shadow Pokemon), which was probably an unintentional side-effect.

So maybe Shadow Pokemon actually are a lot like steroid abusers.
 
Wow, there have been a lot of interesting theories. Some even I hadn't considered before, like that Celebi doesn't "heal" the pokemon but reveses time so that it was never turned into a Shadow pokemon. That's a pretty novel thought.

To throw my own hat into the mix, I want to connect Shadow Pokemon to infinite energy and primal reversion. Let's start with some knowns:

1. Orre is a desolate wasteland without any natural pokemon, save for a few tiny oases in XD.
2. Primal Reversion and Mega Evolution use infinite energy (amongst other things) to power up the pokemon. Some uncommon changes include a change in type, and some rarer changes are new attacks connected to the reversion/mega evolution.
3. Soylent green is people infinite energy is made of dead pokemon/life energy.
4. Mega Evolution and Primal Reversion have emotional connections (Mega evolution is stated to be based on trainer bond, Primal reversion caused Groudon/Kyogre to act more... primal. Granted, they were already in a grumpy rage to begin with, and you the player can cause primal revert with no consequences).
5. Primal Reversion is is mostly a power level and color change, unlike mega-evolution which is a full transformation.
6. Shadow pokemon will naturally heal given any trainer with a heart, poke-therapy just speeds the process up (the shadow gauge decreases in battle).
7. The exception is XD001, Shadow Lugia, who has had a color change in addition to aura and moveset change.

So what do I take from all this? Shadow pokemon are a small-scale artificial primal revert caused by pokemon forcibly absorbing infinite energy. Since infinite energy is made from pokemon, maybe this is like a philosopher stone and takes some of the emotions of the pokemon absorbed with it. This chaotic concoction causes pokemon to close their hearts due to either the rage of these past lives, or as a safety measure against them. One point to mention is that Shadow Pokemon aren't emotionless, as when the go into hyper mode

Since no mega-stones were used as a proper channeling device, Shadow Pokemon ended up different than a true Mega or Primal. For one, the energy will leak out over time (either by tender love and care, or just naturally through battle). And another, the infinite energy is expressed more as a moveset change to Shadow Type, supereffective against everything else. But refining the Shadow Pokemon process created XD001 - Shadow Lugia, which looks closer to a primal reversion. It's still not complete though, as it has defects (hyper mode/reverse mode, no EXP) but a one-type super coverage move was too tempting to pass up. Especially given the stronger shadow moves, like Shadow Half and Shadow Rave or Shadow Blast.

The big question would be where would they get the infinite energy. To answer questions with questions, why do you think Orre is mostly a barren wasteland? (O_O)

Now naturally this theory still has holes. Primal Reversion for one isn't necessarily bad, and is stated to be drawing on the natural energies of creation (even though we just saw Kyogre/Groudon go get crystallized infinite energy). And the "lingering emotions" bit has absolutely no evidence. Still, what do you guys think?
 
It's not natural for Pokemon to become Shadow Pokemon.
While this is true, what particular abilities do the thus unnatural Shadow Pokemon exhibit that a normal Pokemon could not theoretically in some kind of Fight-or-Flight situation? The only thing that comes to mind the Shadow moves themselves, which still aren't totally consistent and thus could still be influenced by the Pokemon species.

I do think there's some merit to be had with the connection to Adrenaline/Fight-or-Flight state of mind. The original Shadow Rush essentially amounted to being Take Down, only cruder, able to hit anything neutrally to dissuade the assault, but damaging the user slightly in doing so. It reminds me a bit of a more feral/extreme version of Mystery Dungeon's Basic attack, which most Pokemon didn't use except in desperate situations since it was better to outmaneuver or outsmart the opponent with moves. Hyper/Reverse Mode would be the result of a totally feral state of mind, blocking out the trainer's orders and further favoring Shadow Rush, between the Criticals which consequently cause more recoil, or non-battle actions such as attacking the trainer. Reverse mode outright hurts the Pokemon for being in it, akin to some animals pushing their bodi The actions that bring a Pokemon out of that state are massages or Calls, the former relaxing and the later breaking the haze to help them focus.

Along this line, being a Shadow Pokemon at all removes the inhibition towards the fight-or-flight state. A "fresh" Shadow Pokemon stays out of Hyper/Reverse Mode often because they're still closest to the most feral state as a "norm". As they're purified, the Pokemon calms out on the whole, but still has the hair trigger as a result of regaining their senses after the shift, which is why they go back into the Fever Pinch more easily as they're more purified.

I don't think think we can connect Infinite Energy with the Colosseum games since they take place in two different time lines.
Technically, is there anything to confirm that Colosseum's events did not also happen in the ORAS timeline? We played the version tied to the original RSE, but that doesn't mean it didn't happen in others, merely that we didn't see them because replaying the exact events again (which would still have to use the same 48 Shadow Pokemon) wouldn't make for a worthwhile product just for the Gen 6 mechanics update.

While Mega Evolution was never outright discovered by most humans in the RSE, is there any outright proof it doesn't exist? Cipher's "tools only" perception of Pokemon wouldn't make it far-fetched for them to come into the discovery at the expense of Pokemon lives, but with less means and more malevolent intentions than AZ did in constructing the Ultimate Weapon. When that energy becomes widespread knowledge from scientifically making Pokemon Feral beasts instead of through causing Mega Evolution by a bond with the Trainer companion, it paints it in a more "off limits" light to even think about. Imagine if fire was rediscovered, but its first use was the flamethrower rather than the steam engine, for example. The first use of a phenomenon can color people's perception of it even if there are other uses to be found.

Wow, there have been a lot of interesting theories. Some even I hadn't considered before, like that Celebi doesn't "heal" the pokemon but reveses time so that it was never turned into a Shadow pokemon. That's a pretty novel thought.

To throw my own hat into the mix, I want to connect Shadow Pokemon to infinite energy and primal reversion. Let's start with some knowns:

1. Orre is a desolate wasteland without any natural pokemon, save for a few tiny oases in XD.
2. Primal Reversion and Mega Evolution use infinite energy (amongst other things) to power up the pokemon. Some uncommon changes include a change in type, and some rarer changes are new attacks connected to the reversion/mega evolution.
3. Soylent green is people infinite energy is made of dead pokemon/life energy.
4. Mega Evolution and Primal Reversion have emotional connections (Mega evolution is stated to be based on trainer bond, Primal reversion caused Groudon/Kyogre to act more... primal. Granted, they were already in a grumpy rage to begin with, and you the player can cause primal revert with no consequences).
5. Primal Reversion is is mostly a power level and color change, unlike mega-evolution which is a full transformation.
6. Shadow pokemon will naturally heal given any trainer with a heart, poke-therapy just speeds the process up (the shadow gauge decreases in battle).
7. The exception is XD001, Shadow Lugia, who has had a color change in addition to aura and moveset change.

So what do I take from all this? Shadow pokemon are a small-scale artificial primal revert caused by pokemon forcibly absorbing infinite energy. Since infinite energy is made from pokemon, maybe this is like a philosopher stone and takes some of the emotions of the pokemon absorbed with it. This chaotic concoction causes pokemon to close their hearts due to either the rage of these past lives, or as a safety measure against them. One point to mention is that Shadow Pokemon aren't emotionless, as when the go into hyper mode

Since no mega-stones were used as a proper channeling device, Shadow Pokemon ended up different than a true Mega or Primal. For one, the energy will leak out over time (either by tender love and care, or just naturally through battle). And another, the infinite energy is expressed more as a moveset change to Shadow Type, supereffective against everything else. But refining the Shadow Pokemon process created XD001 - Shadow Lugia, which looks closer to a primal reversion. It's still not complete though, as it has defects (hyper mode/reverse mode, no EXP) but a one-type super coverage move was too tempting to pass up. Especially given the stronger shadow moves, like Shadow Half and Shadow Rave or Shadow Blast.

The big question would be where would they get the infinite energy. To answer questions with questions, why do you think Orre is mostly a barren wasteland? (O_O)

Now naturally this theory still has holes. Primal Reversion for one isn't necessarily bad, and is stated to be drawing on the natural energies of creation (even though we just saw Kyogre/Groudon go get crystallized infinite energy). And the "lingering emotions" bit has absolutely no evidence. Still, what do you guys think?

My theory on Primal Reversion vs Mega Evolution is this. Mega Evolution is a Pokemon going beyond what is a "natural" state as a result of the energy, which is probably why some of the forms aren't practical evolutions: they're designed to prevail in battle, as that's the only time a Pokemon would take that form in existing.

Primal Reversion is, as named, the Pokemon returning to a state it naturally had before. Lorewise, Primal Groudon is just "Groudon", while what we know as normal Groudon is "Groudon Repressed" or something similar. My memory's a bit hazy on the legend itself, but as I recall, Rayquaza defeated Groudon and Kyogre and forced them out of their "primal" states. For that to take, they obviously don't have the ability to take the energy back in at such a rate as to turn back.

In both cases, the Stone/Orb is a catalyst for the Pokemon to transform, but Groudon's and Kyogre's states are natural, hence why they transform immediately and without any trainer input at all as soon as they come out, whereas the Mega waits for trainer's command to shift. That said, Groudon and Kyogre cannot naturally maintain their Primal forms regardless, hence why they transform back after the battle and simply revert every time. Whatever happened with Rayquaza, they cannot permanently become their original forms anymore. The Cave of Origin becomes their destination because it is the only place where they can naturally retain their primal form as in the battle with the player.
 
My theory on Primal Reversion vs Mega Evolution is this. Mega Evolution is a Pokemon going beyond what is a "natural" state as a result of the energy, which is probably why some of the forms aren't practical evolutions: they're designed to prevail in battle, as that's the only time a Pokemon would take that form in existing.

Primal Reversion is, as named, the Pokemon returning to a state it naturally had before. Lorewise, Primal Groudon is just "Groudon", while what we know as normal Groudon is "Groudon Repressed" or something similar. My memory's a bit hazy on the legend itself, but as I recall, Rayquaza defeated Groudon and Kyogre and forced them out of their "primal" states. For that to take, they obviously don't have the ability to take the energy back in at such a rate as to turn back.

In both cases, the Stone/Orb is a catalyst for the Pokemon to transform, but Groudon's and Kyogre's states are natural, hence why they transform immediately and without any trainer input at all as soon as they come out, whereas the Mega waits for trainer's command to shift. That said, Groudon and Kyogre cannot naturally maintain their Primal forms regardless, hence why they transform back after the battle and simply revert every time. Whatever happened with Rayquaza, they cannot permanently become their original forms anymore. The Cave of Origin becomes their destination because it is the only place where they can naturally retain their primal form as in the battle with the player.
I don't have any thoughts on Primal Reversion (yet) but I always thought that Mega Evolutions were the Pokemon being placed in its absolute worst-case scenario for a temporary amount of time. The energy for this transformation is supplied by the reaction between Mega Stone and Mega Ring (or whatever you put down in Oriolus' thread). These states aren't viable for the current time period because the developments that the Pokemon undergo (Beedrill's massive power increase) may not be viable in a current environment for a prolonged period of time, but they can work short-term because most enemy Pokemon will be unprepared for change on this scale. The stones themselves are most probably meteoric, which I'll get to next.

Rayquaza is a special case. It has a mikado organ, as the ORAS guy identified. This mikado organ probably developed in Rayquaza because it might not always have a Trainer, but it could still be placed in life-threatening danger that requires the power of its Mega Stone. Swallowing meteorites as it flies through the upper atmosphere/space keeps its mikado organ "vitalized", I guess.

Now, what I want to know is if other Pokemon have a mikado organ as well, or is it Rayquaza-specific. What if the organ was a vestigial structure (maybe in the brain?) that was restored by the energy of the Mega Stone and the Mega Ring?
 

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