Typically, Harry Potter is at the center. He has the hero's role and his connection to the Phoenix makes him a natural fit in any Dark Phoenix fanfiction. Neville Longbottom could be a main character as well. He has shown great courage and growth throughout the original series, and in a Dark Phoenix story, he could play an important part in the fight. Luna Lovegood might also be featured. Her unique perspective and knowledge of the wizarding world's more esoteric aspects could be valuable in dealing with the Dark Phoenix. And Severus Snape, with his complex character and skills, could be a key figure, either trying to stop the Dark Phoenix or being involved in its creation in some dark plot.
Harry Potter himself is often a main character. Since he has a connection to the Phoenix through Dumbledore's Phoenix, Fawkes. He might be the one to face the threat of the Dark Phoenix. Hermione Granger could also be a main character. Her intelligence would be crucial in trying to understand and combat the Dark Phoenix. Ron Weasley might be there too, providing his loyalty and friendship. Another character could be Draco Malfoy, perhaps in a situation where he is either an ally or an adversary in the face of the Dark Phoenix.
One of the main characters is usually Harry Potter, as he is the protagonist of the original series and has a special relationship with the Phoenix. Ginny Weasley could be important too. She has her own strength and in a Dark Phoenix fanfiction, she could be involved in the action, maybe even having a special connection to the Dark Phoenix. Sirius Black, if the story has some time - traveling or alternate universe elements, could be a main character. His wild and brave nature would be interesting in the context of a Dark Phoenix story. And Albus Dumbledore, even in fanfiction, his wisdom and power could be a major factor in the fight against or understanding of the Dark Phoenix.