Some spoilers ahead xD; Not 100% canon, but more experimentation with N's childhood- specifically, his relationship with Ghetsis.
In the beginning, there were three.
Only two had raised his son. Anthea and Concordia, Love and Peace. Sisters whose very identities were perfect compliments of one another. But the balance between them had been far more passionate, far more beautiful.
Her name was Harmonia, and from the moment they met, Ghetsis was smitten.
She dreamed of a world where Pokemon and people could coexist without fear of conflict- and she continued to pursue that ideal even after the birth of their son, traveling to distant lands to make bold statements and a change. Back at the castle, Ghetsis did his best to impress the importance of those values upon the boy who drank in his every word. He promised himself that when she returned, her son would be perfect.
He couldn't help a vague sense of disappointment that N had inherited more of his features than hers, but it was only a fleeting thought.
"Mama's on TV, N," he cooed, guiding his boy towards the chair to watch. This was standard procedure- whenever reporters covered Harmonia's latest demonstration, she would phone them from the nearest Center so they were sure to see it. She always added a little wave and a whispered I love you just for the two of them when it was over and done. He loved hearing that from her, but seeing the way N's green eyes brightened made it even more magical.
That was one thing he shared with her, at least. Those beautiful eyes.
He grinned, watching his son scrabble up the side of the chair to perch on his lap, eyes already glued to the screen. It was a commercial break, an ad for the supposedly "revolutionary" new Pokeball. The all-new Timer Ball! The longer the battle... Ghetsis cannot remember exactly how the sentence ended anymore, and it kept him awake at night for weeks after the realization. Everything about that moment had been burned into his memory, and letting it slip away felt oddly, uncomfortably close to giving up.
Because seconds later, he heard his wife's last words through a TV screen.
N was too young to understand, he knew. At three years old, how could he possibly process the fact that his mother was gone, slashed open by a Pokemon, a monster a thousand miles away? But Ghetsis was haunted by the impossibility, the finality.
We have nothing to fear from them. Here, I'll prove it to you.
How many times had she said those words before now? How could they have failed? (And did he even say I love you before she left?)
It was amazing and terrifying, the things he could no longer recall and the details he could not escape.
The hardest part was N. Watching the little ghost of her ideals run around the castle without a care in the world, he couldn't help but wonder. How could he reverse this love? How could he explain what they did to her? (Why did it have to be green hair?)
N's adoration for Pokemon was irrevocable, he realized. His friends were far more easily understood than the abstract of a mother who'd been missing in more ways than one. But maybe it could be changed. Maybe it could be used to further a new ideal, one that would prevent others from suffering the way he had.
And so the beautiful, intricate illusion began.
"Where is she, Papa?" N asked one day, cocking his head to the side. "She's usually home by now."
"Mama's busy now," Ghetsis replied, taking care to conceal red-stained hands and burned skin under his elaborate robes, "but she sends you her love and a present." He hated the way his boy's eyes lit up at that. Those green eyes so unbearably like her. So before he could speak again, the sage presented what he had come to deliver.
It was a Darumaka, and it was bleeding.
"P-Papa! It's hurt!" N cried, backing away in horror.
"This is what trainers do to their Pokemon," Ghetsis explained, crouching beside his son- their son. "But you'll be a powerful man one day. You can change them."
"When I'm in charge," the green-haired boy whispered, crawling forward again to stroke the trembling Fire-type's fur, "trainers and Pokemon will never have to meet."
His father only nodded in approval, then turned towards the door, tossing a few words over his shoulder as he went.
("I always knew you'd be a good king.")
As N grew older, started to travel the region, he began to ask questions.
"Father, what's my last name?" he questioned through the Xtransceiver after one too many encounters with the strange girl from Nuvema Town. The sage struggled to mask his irritation and alarm- if N gave away such information to anyone, especially a trainer, the ideal he had worked so hard to make a reality could be ruined.
"I don't know what you're talking about."
"Touko has one."
"I think you're confused," he said slowly. "Trainers can't be trusted."
"Her Pokemon told me when I tried to hear its voice. Pokemon don't lie."
"Harmonia," Ghetsis replied. N smiled gratefully.
If any memories stirred at the name, he didn't show it.
The dream ended in fire and a collision of myths.
They asked him why, and for the first time, he hesitated. Defeat was inevitable, but weakness was not. He would lose this battle as gloriously as the dragon who had fallen before him, and he would be conquered with none of the honesty that plagued his twisted boy. How could he show them the broken man whose desire for power abandoned him so long ago? The desperation that clawed at his insides, screaming for justice even as he fed his son the lies?
No, these people wanted someone truly evil. They waited patiently for him to rant and rave, to reveal some inner turmoil so unlike the one that lurked behind those dark eyes. So he gave them what they expected to see. He screamed until his voice was hoarse, husky with emotion and exhaustion and emptiness that they failed to see or understand, writing off the truth as a convenient lie. He turned to his son and he tore him apart, hurling insults and pouring all his shame into a boy, a boy with green hair that he wished was blue, when all he really wanted was to see those eyes one final time before they took him away forever.
They never asked the most important question- they were convinced they already had the answer.
(Convenient lies, but who are you lying to?)
I'm not sure how I feel about this one, to be honest xD; Maybe I'm the only one who thought this way, but "Ghetsis Harmonia" never really sounded right to me. And I couldn't help but notice some similarities with the names Anthea and Concordia...
Anyway, this is obviously more of a fan interpretation than anything, and I don't consider it the most logical explanation. But if the game refuses to give me information on N's backstory, I'll just have to make it up for myself xDD