A power - hungry warlord from another dimension could be the main antagonist. He notices the unique connection between Naruto and the Supreme Kai of Time and sees it as a threat to his plans of universal domination. He uses his advanced technology and some stolen time - based magic to try and disrupt their bond and conquer both their worlds. He has an army of powerful minions and is constantly devising new strategies to outwit Naruto and the Supreme Kai of Time.
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.
It could be Salem herself if the fanfiction focuses on Naruto trying to stop her evil plans. Since Salem has a long history of causing chaos and destruction, Naruto would see her as a force to be reckoned with and try to oppose her.
It could be a rogue ninja from an old clan who has a vendetta against both Konoha and Kumogakure. This ninja has been gathering power in secret and plans to destroy both villages to avenge his clan's past defeat at the hands of the combined forces of the two villages.
In this fanfiction, it could start with the Supreme Kai of Time observing Naruto's world from afar. She becomes intrigued by his unwavering determination. So, she decides to make contact with him. Naruto, being the curious and brave character he is, accepts her offer to learn about her powers. As they interact more, they find that their combined powers can be used to stop an ancient evil that was once sealed away but is now starting to break free. This would involve Naruto learning about time - space ninjutsu in a whole new way and using it in tandem with the Supreme Kai of Time's abilities.
It could be the other demons who oppose the Queen of Demons' newfound alliance with Naruto. They might see Naruto as a threat to their way of life or as a tool that the Queen of Demons is misusing. So, they would try to break their bond and destroy Naruto.
Maybe a dark ninja clan that has a grudge against Naruto and also wants to control the Vampire Queen for her powers. They would try to set traps for both Naruto and the Queen, making it difficult for them to trust each other and work together against the real threat.
It could be a character like Orochimaru who somehow gets access to Gotham's technology and becomes even more powerful. He could be creating new types of jutsu using the advanced tech there and causing chaos in both worlds.