We all know about Wally. The sweet little kid from Petalburg, who first showed you how to catch a Pokémon in the tall grass. Throughout the games Ruby, Sapphire, and Emerald, he's leveled up the Ralts he caught that day in hopes of defeating you and proving his worth to himself. But there have been a few inconsistencies about his very existence.
N is much of the same case. He's one of your main opponents in the games Black and White, focusing on the liberation and feelings of Pokémon, not their human counterparts. He also possesses the unique ability to speak with Pokémon; a trait never before seen.
In truth, both of these characters' puzzling backgrounds are answered in the same story. And this story begins not in Unova, nor Hoenn, but Kanto.
Gideon, a scientist and a member of Team Rocket, was part of the crew assigned to create a clone of Mew. He was one of the leaders of the experiment, and the first to flee when Mewtwo escaped and went on a rampage. However, rather than be terrified of the monster he had created, Gideon was fascinated and inspired to continue his research, despite the casualties the escaped Mew clone had caused. He immediately began to work, though this time, with Pokémon from faraway corners of the world.
His choices in DNA samples required the Pokémon to be imported. So, within a week of starting his new project, he acquired, no doubt, illegally, a female Kirlia and a male Zorua.
Gideon chose these Pokémon for their high stats and incredible movesets, many of the moves of which are shared between the two. However, they were unable to breed and create an egg. Kirlia belonged to the Amorphous Egg Group, while Zorua was exclusive to the Field Egg Group, thus rendering them incompatible. But Gideon didn't give up. This was merely a small hurdle in his experiment, and as Mew didn't lay eggs at all, he knew how to construct a being from DNA samples alone.
Unlike Mew, Kirlia and Zorua didn't have the genetic makeup allowing for adaptability. There was only one method by which he might simulate that unstable DNA coding.
Both Kirlia and Zorua reach their final stage at Lv.30. So, obtaining a large amount of rare candies, he leveled them up until they began to evolve, then mid-evolution, he took their DNA samples, thus getting unstable DNA of both Gardevoir and Zoroark.
Using similar methods to the Mew Project, Gideon began to create a Pokemon from DNA alone. But with the unstable evolutionary DNA, he was able to fuse the two together. It was slow going, but the end result amazed him, defying all logic and accumulated data.
Within the clone growth chamber was not a Pokémon, but a human boy.
When the evolutionary DNA had fused together, they were meant to be incompatible. So, to compensate, the Zoroark DNA, famous for its ability to change form, morphed to be something more like the Gardevoir's DNA, the end result appearing in nearly every aspect to be human.
The human boy was pale, with pastel green hair and blue eyes signifying his heritage. But when he underwent the tests and scans, they indicated that although he was human-like in appearance, his DNA was completely that of a Pokémon.
Gideon was thrilled in his discovery, and as soon as he could, began testing the boy's abilities. Unfortunately, they did not bode well. The boy's DNA remained unstable, and he was unable to provide sufficient antibodies to combat disease. As such, he often fell ill. Aside from this, his ability was proved to be Synchronize, which only gave defense if the user was hurt first.
The boy also seemed to have gotten the short end of the stick in the stats accumulated from both parents, having low HP, Attack, Defense, Speed, Special Attack, and Special Defense. Beside Confusion, Growl, and Tackle, he was unable to learn any moves, even from TM or HM. Combined with his low stats and failing health, he was a useless Pokémon indeed, aside from his humanlike ability to speak. He was deemed a failure by Gideon, and confined to prevent escape.
The boy was something to work off of, though. Taking his first experiment's DNA, Gideon combined them with the DNA collected from the Gardevoir and the Zoroark, strengthening the stability of the genetic coding. A new boy was soon grown. He looked much like his predecessor, but his eyes and hair were slightly more vibrant. The tests Gideon simulated on him proved that this experiment was the end result he was looking for. The second boy never fell ill once, having the highest of both parents' stats, with an Adamant nature and the ability Illusion, allowing for a camouflage defense like his Pokémon father, His moves were Destiny Bond, Memento, Shadow Sneak, and Misty Terrain.
Eventually, in a final test of ability, the second boy was pitted against the first. Yet, unbeknownst to Gideon, both boys had acquired emotion, despite preventative isolation. Neither was willing to fight their own kin. Thinking quickly, Gideon came to a solution- one which would force them to fight.
"You two will fight. The winner will live while the loser dies. Choose not to fight, and I will dispose of you both. You're not irreplaceable. I can make more of you."
The two of them had to fight for their lives, and it was obvious who the victor would be before the match even began. The second boy easily defeated the first. The prototype boy was abandoned to the wild to be preyed upon by the wild Pokémon, despite the second's protests.
At the time, a certain family was camping in those very woods. Wendy of Verdanturf Town, along with her parents, uncle, and aunt, were on a picnic when the experimental boy stumbled into the clearing. Wendy's family took him in, her uncle and aunt claiming him as their son while occasionally switching custody of him with her parents for his health.
He was given the name Wally.
Wally's time in Gideon's laboratory, being forced to fight and called useless and weak took its toll. As such, Wally most definitely lived up to his Pokémon-born Timid nature. He seldom spoke, and when he did, it was almost always with a stutter or hesitation, and was always well-mannered.
When he was ten years old, as indicated by Pokémon Trainer rules, he obtained his license, borrowing a Zigzagoon of your father's, his first encounter being a wild Ralts, the most elusive out of the Pokémon in that area. On the first try, he caught it.
According to the Pokédex, "Ralts senses the emotions of people using the horns on its head. This Pokémon rarely appears before people. But when it does, it draws closer if it senses the person has a positive disposition." Wally, technically, is not a human. Therefore, it would be completely logical that a Ralts would immediately appear before him. If they can sense emotions, they would naturally be able to sense that he's one of them.
Throughout his adventure alongside you, Wally challenges you to battles. Neither in his intro nor his outtro has he ever been mean spirited toward his Pokémon or you. Perhaps it's because he knows what it feels like to battle and lose.
The second child was praised for his excellence by his creator. Gideon gave him more and more challenges to overcome, against every type of Pokémon discovered. As a tri-type, being Psychic/Fairy/Dark, the boy was able to best every hurdle he was given. He began to grow very powerful under Gideon. This wasn't a problem...until the boy began to disobey orders.
We're all well-aware of what happens when a Pokémon is caught or traded at too high of a level for the current number of badges with which to exercise control with. This very phenomena, known as the Rebel Syndrome, happens when a Pokémon begins to second-guess their trainer's strength. And as the experimental boy began to grow in level, he exhibited Rebel Syndrome, only listening to Gideon when he felt it in his best interests.
When the Rebel Syndrome set in was when Gideon began to, for the first time in his life, fear his creation. It was rather ironic that a scientist from the infamous Team Rocket would fear a five-year-old child. But that five year old child was currently at a level 74, and the Rebel Syndrome was fully within the young boy's mind. When one day, he intentionally struck the scientist with a Night Daze attack. Panicking, Gideon locked the child in his cell, lit the laboratory on fire, and fled, fearing that somehow the Pokémon child might escape and come after him.
In the ruins of the fire, only one creature was left alive. The boy had used every last ounce of his power to maintain a strong Protect bubble around himself. When the last ember had died, he finally dispelled it, exhausted. With nowhere to go, the child went into the woods, hoping, maybe, his predecessor and brother might still be alive. He searched for months, but with no luck.
Two years later, in the Unova region, the mastermind Ghetsis stumbled across a young, nameless boy, accompanied by a Darmanitan and a Zorua. The boy was very distrusting of humans. This suited Ghetsis very well. To gain the boy's trust, he claimed to be his father, who had been long searching for him. But the boy knew differently, and told his true origins, and of Gideon. Ghetsis denied these claims. He said that Gideon had stolen the boy as an infant, and he had been searching for the child all the while. With his insistence, the boy came to believe the man. Ghetsis took him in, and had his men, members of the alpha-stage Team Plazma, before it was known to the world, scan him. It was indeed as he had said about being a Gardevoir/Zoroark hybrid.
Because of this, the boy was named Natural Harmonia Gropius, which translates to Natural harmony's structure, referring to his perfection as the final result of the Gardevoir/Zoroark experiment. Although Ghetsis adopted two girls, Anthea and Concordia, to care for him and teach him the ways of the world, he retained two things.
His ability to speak with Pokémon.
And his constant desire for Pokémon to be freed from what he'd suffered.
The next time you roll your eyes at the screen when Wally challenges you to a fight, mentally criticizing him for his weakness, or button mash to get through N's dialogue so you don't have to read it all, remember what they've gone through in their lifetime. They merely don't want to have history repeat itself.