Perhaps one of the Kiri's high - ranking officials who believes that Naruto's growing influence in the ninja world could be a threat to Kiri's future. So he orders the kidnapping in the name of protecting Kiri. This official may think that by studying Naruto or using him as a bargaining chip, he can secure Kiri's position among the other ninja villages.
There might be a secret organization within Kiri that operates in the shadows. They kidnap Naruto because they think he holds the key to some ancient prophecy that could change the balance of power in the ninja world. They are fanatical about achieving their goals and see Naruto as the means to an end, regardless of the fact that it could lead to war between Konoha and Kiri.
It could be a rogue ninja from Kiri who has his own motives for kidnapping Naruto. Maybe he wants to use Naruto's power to take over Kiri. He sees Naruto as a tool to gain control and doesn't care about the consequences for the relations between Konoha and Kiri.
It could be a power - hungry shinobi within Kiri. This shinobi might see the Sage as a threat to his own rise in the village hierarchy. So, he uses his influence to keep the Sage neglected and also tries to sabotage any attempts by the Sage to gain recognition.
The story could start with Naruto being lured into a trap set by Kiri. Once kidnapped, he finds himself in a prison cell deep within Kiri's territory. The Kiri ninjas might try to interrogate him about Konoha's secrets or his own unique abilities. Naruto, being Naruto, refuses to cooperate. As time passes, he befriends a fellow captive who has some knowledge about Kiri's inner workings. With this new ally, Naruto formulates a plan to break free. Meanwhile, Konoha's search party is facing many obstacles in their attempt to find Naruto in the unfamiliar and dangerous land of Kiri.
The main antagonist could be Shere Khan. He has always been a threat to Mowgli and might see kidnapping him as a way to finally get rid of the 'man - cub'. He could be working with some of his sly jackal minions to carry out the kidnapping.
It could be a young and ambitious Kiri ninja who has grown up seeing the neglect of his village. He might be determined to change the situation and prove that Kiri is not to be underestimated. Maybe he has a special jutsu or ability that he believes can put Kiri back on the map.
In this fanfiction, there might be a Kiri - native ninja who discovers Naruto when he's just a child and takes him in. This character would be an important one, as they would be the one to introduce Naruto to the ways of Kiri. Also, there could be a group of anti - Naruto shinobi in Kiri who see him as a threat to the village's traditions and try to drive him out. They would be antagonists in the story.
Obviously, Red X would be the main antagonist as he is the one doing the kidnapping. But there could also be other antagonists in the background. For example, if Red X was working for someone else, that person could also be an antagonist. Maybe a powerful intergalactic criminal who wants Starfire's powers for his evil plans.
It could be an old enemy of the gods who has been biding their time. Maybe a powerful Titan that was thought to be defeated but has found a way to come back. This Titan could use Percy to kidnap Reyna because she has a connection to a certain power that the Titan wants to use to regain full strength and overthrow the gods once again.
Well, Naruto is obviously one of the main characters. There might also be some original Kiri - nin characters created specifically for this fanfiction. For example, a young and talented Kiri - nin who becomes Naruto's friend or rival.
A rogue shinobi who has a personal vendetta against Sakura or her friends. Maybe this shinobi blames Sakura for something that happened in the past and decides to kidnap her as revenge. He could be a powerful and unpredictable antagonist.
It could be Doji. He's always been after powerful beyblades and Gingka's Pegasus is one of the strongest. He might kidnap Gingka to get Pegasus and use its power for his own dark plans. Another option is Ryuga. Although he has his own code, in some fanfictions he could be desperate enough to kidnap Gingka to prove his dominance in the beyblade world. Also, a new and unknown blader who is jealous of Gingka's skills and popularity could be the antagonist and kidnap him to make a name for himself.