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.
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.
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.
One possible plot could be that Naruto gets transported to Lara Croft's world. He teams up with her to explore an ancient tomb filled with dangerous traps. Naruto uses his ninja skills like speed and agility to avoid the traps, while Lara uses her knowledge of archaeology to decipher the tomb's secrets. Together, they face off against an ancient evil that was sealed in the tomb long ago.
I really like 'Lara's New Companion'. In this fanfic, the reader is a skilled archaeologist who meets Lara. Their shared knowledge and different perspectives create a lot of interesting interactions. The author also adds a touch of mystery to the story, which keeps you hooked from start to finish.
A common theme is the clash and then the融合 of their two different worlds. Naruto's world of ninjas with its unique powers and Lara Croft's world of archaeology and adventure.
It could be Kaguya Otsutsuki. Since she has powerful abilities and a thirst for power, she would see Kefla's power as a threat and Naruto's influence as something to be eliminated. She might try to manipulate events to turn the ninja world against Kefla and Naruto.
It could be someone who wants to merge their two worlds in a chaotic way. Maybe an evil scientist from Leela's world who has discovered the power of chakra and wants to use it for his own dark purposes. He could try to capture Naruto to study his chakra and use it to take over both universes.
The main antagonist could be an evil merman who wants to take over Ariel's kingdom and is also jealous of her friendship with Naruto. He might use his dark water - based magic to try and stop them.
An ancient evil force that was sealed away by Hashirama long ago could be released in Naruto's time. This entity, having a grudge against Hashirama for imprisoning it, would see Naruto as an obstacle too since he's allied with Hashirama. It could have powers that are completely unknown to the modern ninja world.