Another likely antagonist could be a rogue group within Naruto's village. They might have turned against the village's values and see Riasa as a means to an end, like using her as a bargaining chip with other villages or for some personal gain.
Well, perhaps the main plot could be centered around protecting Riasa from some sort of danger. Maybe there are enemies after her, and Naruto, Kiba and Issei have to use their unique skills to keep her hidden. Naruto could use his shadow clones to create diversions, Kiba with his dog companions could sniff out any approaching threats, and Issei might have some special abilities to help with the concealment.
It could be Orochimaru. He might see the potential in the relationship between Naruto and female Kiba as a threat to his plans. Maybe he wants to use their connection to his advantage or simply disrupt it to create chaos in the village.
It's possible that the antagonists are from another dimension. They have sensed Naruto's growing power and want to stop him before he becomes too strong. They are using their unique abilities to track him down while he's in hiding. These antagonists could have powers that are completely foreign to the ninja world, making them very difficult to defeat.
Well, one possibility could be that they are hiding from some sort of danger. Maybe there's a powerful enemy in the Naruto world and in the Issei's world (assuming it's from High School DxD) that they need to avoid. And Risa's place is the only safe haven for the moment. They might be waiting for an opportunity to strike back or for help to arrive.
The other shinobi villages might also be antagonists. If Naruto's village is seen as a threat because of his power, they could target him. This would make Naruto angry as he's being attacked for no good reason other than fear. Their actions against him and his village could lead him to a darker state as he has to fight back against these external threats.
Sasuke could potentially be an antagonist. Even though they were friends before, Sasuke might see Naruto's new fused power as a threat to his own goals or ideals. He could challenge Naruto, thinking that Naruto's power is getting out of hand. Another could be some remnants of the Akatsuki. They might be interested in Naruto's new power and try to either steal it or use it for their own evil purposes.
Naruto could use his explosive - natured jutsus like the Rasengan. If he was sparring with Kiba, a misdirected Rasengan could hit something explosive nearby and cause an explosion involving Kiba. For Issei, if they were in a battle together, Naruto's chakra - infused attacks might react with Issei's energy - based powers in an unexpected way and create an explosion.
It could be an evil version of Sasuke. In the original story, Sasuke had his dark moments, and in a very dark fanfic, he could be fully consumed by evil and oppose Naruto in a much more malevolent way.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
Another way to depict the fear is through their internal thoughts. The author could write in the first - person perspective for each character at times. Naruto might think about how the explosions remind him of the destruction he saw during the Pain invasion and how he doesn't want to see that kind of destruction again. Kiba could be thinking about how his ninja skills might not be enough to protect himself and his dog from the explosions. Issei might be having flashbacks to a past experience where he was nearly killed by an explosion and how that fear has now resurfaced.