The main villain could be a power - hungry Atlantean sorcerer who wants to use the power of Atlantis to rule both the underwater world and the surface. He might see Percy as a threat to his plans and try to eliminate him.
The Titans could still be a major threat. Even though they were mostly defeated in the original series, some of their followers might see Percy's new role in Atlantis as a threat to their plans for chaos. They could try to undermine Percy's position in Atlantis and use the underwater city as a base for a new uprising.
A possible plot could involve Percy being sent to Atlantis on a mission by the gods. In Atlantis, he uncovers a conspiracy among some of the Atlantean nobles who are planning to overthrow the current ruling family and take over the power. Percy then has to decide whether to get involved in the internal politics of Atlantis or just focus on his original mission. Along the way, he also learns about the unique culture and magic of Atlantis, which is different from what he's used to in the surface world.
One idea could be Percy having to face a new underwater threat that is specifically targeting Atlantis. Maybe a powerful sea monster that was once imprisoned by the Atlanteans has been released and Percy has to figure out a way to stop it without causing too much destruction to the underwater city.
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.
Obviously, Percy Jackson is one of the main characters. He is the son of Poseidon and has his own set of powers and a strong sense of justice. Another important character could be the current prince or princess of Atlantis. They might be Percy's ally or rival, depending on the story.
He might discover new sea creatures that are unique to Atlantis. Maybe he'll find a hidden school of magic there, or encounter ancient sea gods who have been forgotten by the outside world.
Maybe Percy is sent on a quest to Atlantis because there are rumors of a traitor among the Atlanteans who plans to side with the Titans. Percy has to navigate the complex political situation in Atlantis and figure out who the traitor is before it's too late. He also has to deal with the Atlantean magic which is different from what he's used to.
One interesting plot could be Percy exploring the hidden, ancient parts of Atlantis that are full of forgotten magic and powerful artifacts. Maybe he discovers a long - lost prophecy that only he can fulfill, which involves uniting different sea - based tribes in Atlantis.
Well, it could involve Percy having a unique connection to the lost city. Maybe he discovers some ancient powers there that are tied to Atlantis' history. He could meet Atlantean characters who have been waiting for his arrival, thinking he's some sort of prophesied hero.