A unique exploration could be that Naruto's fear of the dark is actually a manifestation of a deeper fear of the unknown. The dark represents all the things he doesn't understand or can't control. In the fanfiction, he meets a mysterious character who lives in the dark and has to learn to face this character and his own fear in order to gain new powers or knowledge. For example, the character could teach him a new jutsu that can only be learned in the dark if he can overcome his fear.
The fanfiction could show Naruto's fear of the dark through his dreams. He could have recurring nightmares about being in a pitch - black void, unable to move or use his jutsu. This would be a unique way to explore his internal struggle with this fear without it being too obvious in his waking life at first.
It could show Minato experiencing Naruto's loneliness as a child first - hand when in Naruto's body. This would make Minato understand Naruto's pain on a deeper level. Then, when Naruto is in Minato's body, he could see how much his father was respected and loved, which would strengthen their bond in a new way.
One way is by delving into his past traumas more deeply. For example, his loneliness as a child could be explored further to show how it led to his trust issues. Maybe in the fanfiction, Naruto has a series of flashbacks that make him question every new relationship he forms.
Some fanfics might explore their relationship by giving them a shared mission. They have to work together to save the village or something similar. During this mission, they get to know each other better, not just as mother - son but as comrades. They learn about each other's strengths and weaknesses, which deepens their bond in a very unique way.
Another unique exploration could be through a shared goal that is not related to the main Naruto plot. For example, they both want to protect a special place in the spirit world that has significance for the Nine - Tails. To do this, they have to work together in a way that they haven't before. Naruto has to use his human skills and the Nine - Tails has to use its tailed - beast powers in harmony. This would show a different side of their relationship, one based on mutual respect for each other's abilities.
One way is by exploring their cultural differences. Vegeta is from an alien race with its own values and traditions, while Bulma is an Earthling. The fanfiction could show how they introduce parts of their respective cultures to each other and how that enriches their relationship.
A 'dark not evil Naruto fanfiction' can be unique by having Naruto's 'dark' aspect be something completely unexpected. For example, instead of the typical dark powers like those related to death or destruction, it could be a power that is dark in appearance but has a very positive effect. Maybe he has a power that looks like it's sucking the life out of things, but in reality, it's just absorbing negative energy and converting it into positive energy. This would be a unique take on the 'dark not evil' concept.
Well, it might explore the idea of milk as a source of chakra. In the Naruto universe, chakra is everything. So if milk can boost or replenish chakra in some unique way, it can change the dynamics of battles and relationships. For instance, Naruto could share this special milk with his friends to make them stronger for an upcoming war.
His body language could show it. For example, he might tremble slightly, his hands could be clenched, or he could have a worried look on his face. This would be a simple and direct way to show his fear to the readers.
Naruto could have a snake summoning contract instead of toads. This would completely change his combat style and the types of allies he has. He could summon different kinds of snakes with various abilities like poison, constriction, or even the ability to fly.
A way is by having them switch roles. Naruto could be the one with the burden of a dark secret like Itachi had, and Itachi could be the one trying to bring Naruto back to the light. This role - reversal can show a different side of their personalities and how they interact.