(A small note! To enhance the protagonist's background since he is nameless in the game as with most Shin Megami Tensei games, I use a lot of background from the manga of the same name. The manga was approved by the Atlus staff, and is considered a fleshing out of the main game's story line.)
THE DEATH OF HIS TWIN BROTHER, KAZUYA 
Kazuya and Naoya
resembled each other so much that even their parents weren't able to discern them accurately. Unfortunately, Naoya got sick at a young age and make him feel better, his twin went off to buy a manga while his mother was chatting with friends and was hit by a car, causing his death.
Naoya's guilt inside him continued to
build up for years, and affected his temperament in school. To make sure he remembered who he is, he pierced his ear at the age of 12 so that he doesn't accidentally think himself as Kazuya. Whenever he is stressed or in deep thought, he will without fail start to rub it idly. The earring he wears is a memento; even if his brother is gone, he won't forget him.
For the sake of his lost sibling, he always moves on forward so his brother can be proud of him, especially after he fought against his inner demons and won. It gives him a deeper understanding for his friends who wish to do the same, and in return, he offers them kind words to ease their own inner torments.
PLAYING THE PERSONA GAME 
What started as a
bet between friends about a rumor of being able to see your future if you summoned "Persona-sama" into the world became Naoya's adventure into the mystical and unknown. Gaining the ability to use
Personas from
Philemon, this started a chain of events that would end up with him having to save the world and growing closer to his classmates. He would emerge as their leader, being able to calm them down and keep everyone into a clear path (and trust me they thought about killing each other at one point, hence why he is also known as the 'cat herder'). After gaining the powers of Persona, he lets his raw emotions sometimes push him to do heroic and crazy things to protect others.
DEFEATING KANDORI
Kandori, who they had assumed was their main foe, had gained the powers to essentially become a god. Watching him hesitate to destroy humanity as he had threatened, and then his teammates pointing out the man's weaknesses, made him realize how important it is to be true to ones' self. Being questioned about his plans on what he wants to do, Naoya tells him that he believes in finding his own future - nothing needs to be set in stone, something which gives Kandori peace before his death.
This is also the time when he becomes much closer to his teammates as they realize that their adventure is not quite over yet, and that one of their companions has actually been the cause of everything since the start because she's connected to a special machine, and they've been traveling with an ideal shadow of that sick person.
FACING BOTH OF HIS OTHER SELVES
During their adventures, Naoya had been plagued by someone who looked just like him (minus the earring) claiming to be his brother, Kazuya. In truth, it was the physical representation of his guilt and self-doubt after his brother's death, whose mission was to try and take over Naoya's mind and become the personality 'in control'. After fighting each other, he finally realizes what Kazuya' is, and accepts his shadow as goes back into him and he promises to be a better person continuing forward.
But that's not all! He also has another aspect of himself busy playing video games in his mind, and acting more like a guide, replays all that Naoya done during his adventure, essentially judging him and telling him he did good (saving people even when they were chased by zombies, saving a man at the cost of letting an enemy go, easing Kandori's death and so on). This proof of good leadership grants everyone their ultimate Personas and further solidifies their friendship and Naoya's proof of being a caring soul.
SAYING GOODBYE TO IDEAL MAKI
Once their adventures came to an end, Naoya was the only one who knew the truth - that once everything was fixed, the Ideal Maki that had been traveling with them would return to the real Maki's mind - and just like his other two aspects, would just be aspects of Maki's personality and not like the Maki that had been with them. In a way it was like witnessing the death of a friend, and this Maki didn't help at all by saying "I love you" before teleporting him away from the world they were in as it collapsed.
- The powers of a Persona give its user a stronger resistance to harm (depending on which Persona they are using, this may increase or decrease against certain elements and skills). As an example, Brown, who hadn't activated his persona yet
is nearly bleeding to death while everyone else was mostly unharmed from the attack.
-
Earlier persona users have the ability to detect other users and characters with high magic levels. Their personas 'speak' to them to warm them of what is happening, since, technically their personas are other sides of themselves. This ability would later be given to 'navigators' in the later games and enhanced greatly. You could say that Naoya is more akin to a mini-navigator, he can't see dungeons, and can detect users only if they are somewhat close to him.
- The power to summon Personas. As a protagonist and being granted the power by Philemon himself, Naoya, like his entire team, is a Wild Card user, which means he is able to switch around
multiple Personas (the ones with circles mean he cannot use them apart from the ones marked as such in the Emperor Arcana.
- I've made a
basic list of the ones he'll be using the most. A persona is the ability to summon demons and angels as avatars to do battles with a multitude of skills. Unlike later Persona users, Naoya simply has to raise a hand and summon his Personas.
- The ability to wield swords and submachine guns without much issue
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Character Name: Naoya Toudou
