There might be a group of tomb raiders who are jealous of Naruto's connection to Lara Croft. They see him as an obstacle in their path to obtaining great treasures. Also, some dark forces from both universes could team up. For example, Orochimaru from the Naruto world might make a deal with a villain from the Tomb Raider world to get access to Naruto and his unique powers for their own evil experiments.
Well, it could be about Naruto having some of Lara Croft's skills like her agility and survival instincts in a new world. Maybe he uses his ninja skills combined with her knowledge to go on adventures and solve mysteries.
Lara Croft would probably be initially cautious around Naruto. She's used to being on her own and Naruto's energetic and boisterous nature as a ninja might be a bit much for her at first. But as she gets to know him, she'd start to respect his skills. Naruto would be in awe of Lara's knowledge of different cultures and her ability to handle dangerous situations with ease. He'd constantly ask her questions and try to learn from her. For example, he might ask her how she can climb such steep cliffs without chakra, and Lara would show him her climbing gear and techniques.
It could be a powerful ninja from Naruto's world who has turned evil and wants to use Lara Croft's knowledge of ancient artifacts for his own gain. He might try to force Lara to lead him to the most powerful artifacts so he can become invincible in both worlds.
A powerful cult leader could be the main antagonist. The cult leader believes that the artifacts Lara and Jacob are after have some dark, magical powers that he wants to use to take over the world. He sends his minions after them, constantly trying to thwart their progress and capture the artifacts for his own evil purposes.
The plot could start with Lara Croft finding Naruto in a desolate area. Naruto is injured and alone. Lara, with her kind heart hidden beneath her tough exterior, decides to help him. As she nurses him back to health, she discovers his ninja abilities. She then starts training Naruto in her own way, adding her knowledge of combat and exploration. Naruto, in turn, shows her the power of chakra and ninjutsu. They form a bond and embark on a journey together, where they might search for ancient artifacts that have a connection to both their worlds.
The village elders could be antagonists. They might see Naruto as a threat due to his devil - like origin and try to eliminate him. They fear that his powers could bring chaos to the village.
The Akatsuki could still be the main antagonists. They might see Naruto's new connection to Hades as a threat or a powerful tool they can use. They would try to capture him to either control his powers or eliminate him.
It could be Orochimaru. Since Orochimaru is always after powerful ninja and their abilities, if Naruto is now the son of Asuma, he might see Naruto as a new target with unique potential.
Another possible antagonist could be a rogue Titan from the Titan world who somehow makes its way into the Naruto universe. This Titan could be enraged or corrupted and see Naruto as an enemy because of his mixed heritage. It could cause destruction across the ninja world, and Naruto would have to stop it using his ninja skills and Titan powers.
One possible antagonist could be those who oppose the mixing of the Naruto world and the Greek mythology elements. They might see Naruto as an abomination because of his unique heritage as the son of Demeter. Another could be some of the traditional Naruto villains who now see Naruto as an even greater threat due to his newfound powers related to Demeter. For example, Orochimaru might be interested in Naruto's powers for his own evil experiments.