Some of the die - hard Death Eaters could also be antagonists. They might not trust Harry even with the Dark Mark and try to undermine him or expose his true intentions if they suspect he's not truly on their side. Bellatrix Lestrange, for example, is so fanatical about Voldemort that she would be a likely candidate to oppose Harry even if he seems to be part of the 'dark' group.
There could be some old - fashioned professors at Hogwarts who are against Harry's unorthodox ways of making his mark. They believe in the old - established ways of teaching and practicing magic and see Harry as a troublemaker who is disrupting the order of things at the school.
The Akatsuki could also be antagonists. Since Madara has his own plans with Naruto, the Akatsuki might see this as a disruption to their goals, especially if Naruto is being groomed by Madara to oppose them. They would try to stop Madara from influencing Naruto further.
The main antagonists could be his former friends, like Hermione and Ron. Since Harry is becoming a Dark Lord, they would oppose his new, darker ways. They would try to stop him from causing too much harm to the wizarding world, which would put them in direct conflict with him.
Voldemort could still be a major antagonist, but in a different way. Since Harry is turning to the dark side, Voldemort might see him as a threat to his own power and try to eliminate him. Another could be Dumbledore. If Harry turns dark, Dumbledore would surely oppose him, trying to bring him back to the light. So Dumbledore could be an antagonist from Harry's new dark perspective.
Obviously, Voldemort would be a main antagonist. Since it's the Dark Mark of Voldemort that Harry is forced to take, Voldemort would be pulling the strings, trying to make Harry do his bidding.
Some rogue demigods who are power - hungry could also be the antagonists. They might see the baby as a way to gain more power, like if there are rumors that the child will have special abilities. So they would try to either steal the baby or harm Annabeth to prevent the birth.
Another plot could involve Harry being tricked into taking the Dark Mark. He might think he's doing something else, like a magical experiment or a ritual to save someone. But it turns out it was a setup by a dark wizard. Harry then has to face the consequences, not only the physical and magical changes brought by the Dark Mark but also the change in how others perceive him, especially his friends who might be shocked and scared.
The Hidden Leaf Village elders could be antagonists. If Naruto turns dark, they might see him as a threat to their power and try to stop him. Their actions against Naruto could further fuel his descent into darkness.
The Ministry of Magic could be the antagonists. Since Harry is in a gang, they might see him as a threat to the order of the wizarding world. They could send Aurors after him and his gang mates, trying to arrest them and break up the gang.
Voldemort would likely be the main antagonist still. He might see Harry's potential as an animagus as a way to strengthen his own forces. His Death Eaters would also play a role in trying to convince Harry to join the dark side.