There can be original characters created specifically for the fanfiction. For instance, a detective who is obsessed with bringing down the Joker but slowly starts to lose his own sanity in the process. This character can provide a new perspective on the Joker's reign of terror.
The Nine - Tails also plays a major role. In a dark Naruto story, the Nine - Tails could be more of a corrupting influence, whispering dark thoughts into Naruto's mind and fueling his descent into a more menacing figure in the ninja world.
Naruto himself could be a main character. He might be tempted to use dark summons to gain power to protect his village or friends. For instance, in some fanfictions, he discovers a dark summon that could potentially defeat a powerful enemy threatening Konoha, but at a great cost.
In Naruto dark chakra fanfiction, Sasuke is frequently a central figure. Given his complex character arc and his inclination towards power - seeking, it's easy to envision him being affected by or exploring dark chakra. Naruto too can be a main character. His strong will and connection to positive chakra could be put to the test when faced with the allure of dark chakra. Another character often involved is Kabuto. He has a history of being involved in dark and underhanded schemes, so it's not a stretch to see him in stories centered around dark chakra. There are also some original characters created by fanfiction authors that are specifically designed to interact with the concept of dark chakra in unique ways.
Naruto himself is often a main character. He's usually the one who stands up against the dark guild's evil plans. Sasuke might also be involved, as his power and sometimes ambiguous moral standing can add interesting dynamics when dealing with the dark guild.
Obviously Naruto himself is a main character as he is the one under the dark control. Then there would be his friends like Sasuke and Sakura. Sasuke might be crucial in trying to understand and counter the dark power since he has his own powerful abilities.
Well, obviously Dark Silver himself is a main character. Often Sonic might also be involved as he is a central figure in the Sonic universe. Their interactions can create interesting storylines, like a rivalry or an uneasy alliance.
Naruto himself is often involved. He might be either tempted by Dark Hadou or have to fight against those who use it. Sasuke could also be a main character in such fanfictions. His quest for power could lead him to explore the Dark Hadou. And then there's Kakashi, who with his experience and knowledge, might be involved in trying to stop the spread of Dark Hadou.
Percy is, of course, the main focus. However, in many of these fanfictions, Luke Castellan can also be a major character. Since Luke had his own issues with the gods and turned to the dark side in the original series, he could either be an influence on Percy's dark turn or an ally in his new dark journey. Nico di Angelo is another character who could be involved. Given his connection to the Underworld and his own complex relationship with Percy, he might try to understand what's going on with Percy or try to fight against him if he thinks Percy has gone too far.
Lucy is another character that could be prominently featured. Given her gothic nature, she might have an initial attraction or understanding of the dark arts. She could either be a novice trying to learn more or a bit of an expert guiding the other Loud siblings when they encounter dark arts - related situations.
Obviously, Harry Potter himself is often involved. He's the hero of the original series, so in fanfiction about a dark dragon, he'd be the one to step up and face the new threat. Hermione and Ron would likely be by his side too, as they are his closest friends.