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I feel that there is a misunderstanding about what Mewtwo said and what he actually meant. If looking at it from his perspective, and from his personal experiences, it becomes clear.

He is trying to break through his own mental defense mechanism - (his inability to trust) - by testing N with questions and assessing his response to them. While there is the possibility that he could just read N's mind after hearing such responses, that would make this conversation entirely pointless. (Miracle Eye - either he doesn't know this move, or he chooses not to use it.)

What is really going on here, is this:

Mewtwo knows that N is no longer a trainer, because N told him previously. But he needed to be sure that N wouldn't be tempted by Pokeballs in the future.

Mewtwo doesn't want a trainer, he wants someone he can trust, as both a comrade and a friend. The human part of him would never submit to captivity, but the other side, the pokemon part of him seeks, in biological terms, mutualism with N, because in order to reach the next stage of his evolution - (Mewtwo Y) - and control himself, he needs N as his anker, someone who will not try to manipulate his trust.

Mewtwo is just smart enough to realize that trust is a two way street. It cannot be one sided, both individuals have to be in-sync with the other.
It's a relief to know that somebody else came to the same conclusion that I did about humans being the ones who built most of the mystery dungeons (mainly the ones that follow the rules of basic architecture - aka, Buried Relic.)

(I made that comment about the whole human background stuff back on page 494, but I was pretty sure nobody read/saw it. Still kind of convinced that nobody even remembers what it mentioned.)

But I'm even more surprised that you also had my same suspicions that pokemon were a whole lot different long ago. The Jewel Of Life referred to them as "Magical Beasts," but I'd wager that before even that, they were just "Beasts." No abilities, no special attacks, nothing but predator vs. prey. And then humans came along, and against all logic or reason, decided to take them in and raise them as if they were their own "Family", and teaching them their ways, as well as offensive techniques (TMs didn't exist back then obviously, haha!) which gives legitimacy to what was mentioned during Generation 4 games, where (a long time ago, pokemon and people were one and the same, ate at the same table, etc.) And if any of this is valid, it's no wonder that pokemon have a natural affinity towards humans because it would mean that they owe almost everything about themselves to the humans for helping them evolve to the point were they are able to achieve near impossible feats and use elemental attacks that they were never meant to use.

Also, check out these Pokedex entries ladies and gentlemen!

Kadabra: It happened one morning - a boy with extrasensory powers awoke in bed transformed into Kadabra. source- (Pokemon FireRed)

Yamask: Each of them carries a mask that used to be its face when it was human. Sometimes they look at it and cry. (Pokemon Black&White)

so...technically Abras and Yamasks were once human. let that sink it for a while everyone.
Best Page Ever!
You have no idea how much I love this page! Mewtwo's expression in panel two and ten is just god tier lmao. He's got charcoal on his face XD. And omfg yes, Team A.C.T is back, hell yeah!

And just like most peers in my calculus class, pretty much everybody has absolutely no idea what is happening on the white board. Beautiful, hahah!

"Yep, we're screwed" You're right Wes, if even an Alakazam (They have an IQ of 5000) can't understand it, you know that all hope is lost.

Wow, This is exactly what my study group felt like when we were in calculus IV!

Also, nice job with the diagrams Mewtwo, I know firsthand just how hard it can be to explain vector calculus in layman terms to group of people. It's really damn hard!
@PJSam Well, If Victini was planning to use it to cause mass shadowfication, it's safe to say that there is no way she can use it for that purpose anymore. And besides what I said about blackholes, gamma bursts, and whatnot, there is also the page title "Red Shift", which directly refers to spacial compression/expansion, light refraction, and planetary rotations.

In short, lets just say that I've got a strong hunch that Palkia is extremely pissed off right now lol.
No, it's mass isn't big enough to form a black whole, but for any star that has reached the end of it's life, one of two things could happen: Either it explodes and takes out a large portion of an entire galaxy, or it collides with a blackhole and blasts a giant burst of energy across space (aka, a massive solarbeam!). What's more, blackholes are one of the few things that may possibly exhibit 4th dimensional fluxuations within the 3rd dimension. So basically, Time Travel! :)

This is assuming that the Creation Engine is indeed both simultaneously a Dying Star and a Black Whole that was frozen within some kind of time capsule or something like that. Which would explain why the blast it's shooting off looks like a gamma ray. There is nothing more powerful and destructive in the entire known universe than a gamma ray, and if it is one, they are just lucky that there is even still dirt beneath their feet to even stand on! I mean, if it was firing in the other direction, their planet would have been instantly destroyed.
Holy freakin Pokeballs, that's a gamma ray alright, no question. If Pokemon was more realistic with it's attacks (News Flash, a thunderbolt attack should be enough to kill a human) then they would be vaporized just by standing that close to it.
Whoa, I know that a lot of people are kind of assuming that 'N was a pokemon this whole time wearing a human disguise and doesn't remember anything from his past life due to double jeopardy inter-dimensional mind erasure' but, I think the simple answer is that he's (and I hope I don't offend anybody who actually is one) literally a pantheist bohemian stereotype living in the modern day. In other words, he's a pure nature loving hippie to the 'Nth' extreme. Heheh, I made a pun on his name...praise me!

Basically, he just feels more at one with nature, hence the long hair and his name Natural Harmonia Gropius, also he had a human father, and his name was Ghetsis (I still can't get the game's battle theme from playing back inside my own head after hearing, saying or reading that name and it's haunting my dreams!). And what a great Dad he was, right? A true model role indeed, locking his son inside an exact replica of Richie Rich's bedroom while that haunting background melody keeps playing 24/7. Yeah, is it any wonder why he ran away...? (That's how serial killers are made!)

As for his hidden ability, there have been other humans in the anime with unique abilities, such a Sabrina - a psychic, and Damos from Arceus and the Jewel of Life whose ability I believe more closely matches what N possesses.

And then there's Ash of course...who seems to have an aptitude for everything.

I'm not too familiar with the Ranger games as I'd never played them myself, but in any case, there are only a few ways that the backstory for that could be handled. And all of them mostly depend on whether or not the Rise Of Darkrai and/or Pokemon the Movie: Black/White are canon in this story.

1. Pokemon Black and White Movie: It would have had to happen immediately after that movie, right near the end of the black and white saga for the timeline to add up.

2. The movies are still canon, and Darkrai has been like this for years, whereby him being tortured and experimented on was happening behind the scenes probably during or a bit before the D&P episode where Cresselia appeared and fought him (Which is probably close to or around the time that Tobias acquired him and made him compete in the Pokemon League during the Diamond & Pearl saga, meaning that Tobias might have a minor connection to Cipher.) or somewhere far off into the future.


3. There is more than one Darkrai and more than one Victini, and these aren't the same ones that appeared in the movies or the anime.

Unfortunately, Darkrai has too many appearances in the anime, which sadly means that there is very little wiggle room to work with, so if there really is only one Darkrai, then these comic only events would have to either happen within a very small timeframe or a couple years into the future so that it doesn't interfere with the movies or the anime at all.

Personally, I think it would be awesome and insanely meta if during that one episode in the Kalos season that he trolled Ash and his friends with that nightmare, that he was trying to decide whether or not to turn either Ash or one of his friends into a Pokemon after being forced by Victini to seek out a pure hearted human child to open the door for her, but backed out because of the events that happened in Rise of Darkrai. That would be pure genious in my opinion :)
Dark Type < Fighting Type
Huh...one hit K.O. Must have been a...

Well at least his attack landed and was super effective, unlike my witty and totally un-creative response to this page :(
YES, POKEMON SQUARE! Another practically guaranteed cameo! I wonder if we'll see Team ACT or maybe even Team Go-Getters. Ah, I want to see Felicity's Bank again, and Wigglytuff's old friend area business stand, and also Friend Areas, because heck yes! Seriously, you totally have to show off the old Red/Blue Rescue home base too! And possibly evolution cave. The nostalgia is strong with this one!
@Malc Modnar

Well besides the urge of stating the obvious, (which is that part of it is visible under that hastily drawn gray background o_0) heat energy that is visible at least, is the rapid movement of subatomic particles trying to expand outwards under friction or chemical pressure. If for any reason that those particles were to stop moving, then the rule of quantum physics relating to thermodynamics would break down. This is what the scientific community refers to as, heat death, or rather, one of the eventual ways that the universe will end.

The other possibility, is that this world is nothing more than hollow a reflection of the original world, a dimensional layer existing on top of the current one raised between the 4th and 5th dimensions specifically.

So yeah, that mountain they are currently in, is inside of a different version of the same mountain that exists between the 3rd and 4th dimension. I just blew your mind didn't I lol.
Actually, that may not be the case. The PMD world may exist parallel to the human world, only, humans can't go there, but that would also mean that most of the pokemon that exist there can't visit the human world either. Though for some reason, certain pokemon (I'm guessing that they need to be legendary tier in order to cross between the two worlds) are able to go back and forth as they please. (Heh, no wonder legendary pokemon are so hard to find)

And based on PMSD, and it's representation of the planet earth, I'd say that their world merely overlaps on top of the human world. Which would mean that it's location isn't specifically in Almia, but everywhere at once. Almia was just where the barrier is weakest and easiest to enter from.

@Guest may actually be right about this.
Nope, it's a reference from the games where ghost types were able to phase through walls, but at a price of rapidly draining away your hunger meter.
@Malc Modnar

No...not just their world, all worlds across time and space. In fact, why stop there, with how much he's built up his headcanon, why not make it even more crazy than it already is XD.

Imagine this: It turns out that Miror B really was the true mastermind all along, except he isn't alone. After the fall of Team Rocket, the failure of Team Plasma, and Cyrus's defeat, Miror B. Shows up and rallies all the Teams (Yes, even team Flare) and promises them everything they've ever wanted will become a reality. Ghettsis, and Giovanni both decide to abandon their inferior plans to join forces with Miror B and form Team Vortex!(A Fusion of Team Rocket, Plasma, Galactic, and Flare)

Miror B. is for some odd reason or another, the second chosen one (Think Darth Vader from Star Wars), with Ash Ketchum being the first (Luke Skywalker), and was fated to wield the creation engine, only, that's not what it was...you see Victini was trying to save the world, not destroy it. She was just misunderstood and deeply upset that Cipher took away her V-Wheel, and decided to throw a colossal tantrum, made worse with the fact that she and her bother Darkrai were both infected with the XD Virus (Screw it, throw in Poke'rus too while we're at it.) Miror B's desire was to use the creation engine as the world's ultimate disco ball, and gain all the power in the universe, thus, essentially becoming the pokemon version of whatever the hell Kefka was suppose to be in Final Fantasy VI. And you guessed it, @Dark Matter from Pokemon Super Mystery Dungeon is actually the embodied form of Miror B's magnificent afro given sentience!

And in order to save all existence, all the legendaries from every region must join forces to stop him from forming the infinity gauntlet because reasons. Also Steven Stone, as Iron Man shows up because why the hell not at this point :)
That makes sense. Probably the entire reason why ghost types would avoid the spirit world at all costs is that it is too easy to lose your way. I could imagine that wondering around there for the rest of eternity is the norm, considering it is literally seen as the afterlife/limbo for both Pokémon and humans alike.

Me thinks Gengar made a huge mistake in taking them both there :)
It is a bit strange, but gases can become solids obviously. Usually via temperature changes and other reactions. I'd imagine the temperature in the spirit world would be nothing more than absolute zero (-459.67 F) most likely as there isn't a sun to sustain life (Not that there would be any to begin with.) That's probably where the whole superstitious belief behind an area turning cold whenever a ghost is nearby came from. Under these conditions, practically anything would be turned solid in less than a second. Yeah, that also means that you wouldn't be able to see your breath either since it would be frozen inside of you. Oh, and not to mention that you would die instantly - as in, a frozen stiff. (a dead body - Hah, get it, because he wasn't sure if Darkrai was dead or not lmao.) XD

Heheh, saying that he's feeling a bit stiff is kind of an understatement when you truly think about it lol.
I know I've said this before, but it keeps bothering me for some reason. Buried Relic had to have been built by humans. Theres just no way I could see it any other way. Most structures that are built by Pokémon are just too simplistic and don't reflect the complications involved with building pyramids.

What if the creation engine was made by humans...

That door and it's requirements for access to the creation engine is strangely specific with it needing the wishes or desires of a pure hearted (human) child - though 'child' might refer to other things too, such as mortality.

In a way, it is the perfect safeguard, since it wouldn't open for just anyone, that person must have a pure heart, as in, no selfish intentions. You can't fake something like that.

It makes me wonder if humans at some point in the faraway past have had connection with the legendaries becoming as powerful as they are today. For example, Arceus needs his plates (physical objects) for full access to its powers, and Dialga needs the time gears in order to affect time on a massive scale. And in the Hoopa movie, his unbound form was sealed in an 'object'. This leads me back to a seemingly persistent question that I have always pondered about Pokémon since stuff like this started happening in the anime/movies/games. Where did their powers come from, did they always have these powers, or did someone or something give them their powers.

Here is my off the wall guess: Humans are the ones that originally invented their abilities and teached them how to perform them (Pokémon Masters) through a series of trials (first step: becoming an aura adept) and then manipulating that energy into a specific elemental force. This practice of human magicians, witches, psychics, and etc.) was lost after the great Pokémon war when entire civilizations were wiped out in an instant by the ultimate weapon introduced on Pokémon x and y.

After thousands of years, Pokémon continued passing on this knowledge, (enchanting items such as Orbs, Seeds (Revive Seeds reverting into Plain Seeds after use) rescue emblems, explorer badges, of which they learned from humans before the great purge) and became so good at using their abilities over centuries, that they started being born with them through natural selection, which might explain the concept of egg moves and how attacks can be learned from the parents at birth.

I know people will probably think this is over analyzing things, but seriously, it all somehow adds up. The treasures of Articuno, Zapdos, Moltres. The plates, The time gears. What if, and bear with me here. What if they were made and enchanted by humans?

What if the creation engine was made by humans...

I'm in agreement here, but then, I guess it would make sense if evolutions were influenced by their ages. Otherwise, I'd say they totally lucked out on the RNG gamble. N's form is pretty powerful to start off with too, since he can use illusions that make him look like other pokemon. And Wes can learn bulldoze or earthquake at his evo.

As for Wes, all I can really say about him is crickey mate!
Hence, I didn't say memory loss, I said tampered. (the games only did this because of plot reasons, and also so they didn't have to explain what the protagonists life was like before being turned into a Pokémon.) Jen still had some residual memories, like being human, but there were a few pieces missing, I think?

Also I was just pointing out that there are a large number of characters, that's all. But obviously the more characters there are, means more dialogue and etc.)

Obviously I want this comic to go forever lol, but I'm just trying to stay realistic here.
I don't think you can start out as a fully evolved pokemon though. I am almost 100% confident that Gengar started out as a Gastly, only it is never mentioned simply for the fact that it is an unimportant detail.