It could be a new, powerful Titan that was previously unknown. This Titan might have a vendetta against Percy specifically, seeing him as a major threat to their plans. Maybe they manage to kill Percy, but his rebirth sets in motion a series of events that will lead to their ultimate downfall.
Another possibility is that the main antagonist is a god who has turned against the other gods and demigods. This god might see Percy as a symbol of the old order that they want to destroy. So, they engineer Percy's death. But Percy's rebirth gives him an edge, as he has a new understanding of the gods' weaknesses. He then rallies the other demigods and some of the more benevolent gods to fight against this rogue god.
It could be a new Titan that has been awakened from an ancient slumber. This Titan might be angry at the gods for imprisoning them long ago and wants revenge. Percy's death could be part of the Titan's initial plan to strike fear into the hearts of the gods and demigods, but Percy's rebirth becomes a major obstacle for the Titan.
It could be a powerful Titan who has escaped from Tartarus and blames Artemis for something in the past. So he's out to get her, and Percy has to stop him at all costs, even if it means his death.
The goddess Hera might also be a great antagonist. Since she has a history of interfering in the lives of demigods, she could be jealous or threatened by Percy's rebirth. She might try to stop him from reaching his full potential in his new life or cause trouble between him and his new allies.
It could be an ancient evil that was sealed away long ago but has been released due to Naruto's death. Maybe Naruto's sacrifice in his previous life weakened the seal, and now this evil has emerged. It could be a powerful demon or a dark ninja with extremely strong and malevolent jutsu.
It could be an old enemy from Percy's past life who has also found a way to be reincarnated. This enemy might hold a grudge against Percy for something that happened in their previous encounter and is now seeking revenge in this new life.
Perhaps a powerful and corrupted demigod could be the main antagonist. This demigod might be jealous of Artemis' power and popularity among the other demigods. He devises a plan to harm her, and Percy, being loyal to Artemis, has to give his life to save her from this rogue demigod.
A powerful Titan who has escaped from Tartarus. This Titan blames Percy for his previous imprisonment and wants to make Artemis suffer as well for her role in keeping the Titans locked away. He uses Percy's death as a way to manipulate the situation and turn the demigods against Artemis, or he might try to steal Percy's powers that were left behind after his death for his own evil purposes.
It could be an ancient and powerful Titan that has risen again. This Titan might have a vendetta against Poseidon and targets Percy as a way to hurt him. Since Percy is Poseidon's son, his death in Poseidon's arms would be a great blow to the sea god.
It could be a power - hungry Atlantean noble who wants to rule not just Atlantis but also the surface world. He sees Percy as a threat to his plans and tries to stop him at every turn.
A new and powerful demon that has emerged from the darkest corners of the underworld. This demon is bent on using Percy's connection to the overworld to break through the barriers between the two worlds and unleash chaos. It has powers that are different from what Percy has faced before, like the ability to manipulate the very essence of the underworld's environment.