The antagonist could be a new, self - proclaimed ninja god who wants to rule over all the villages. He sees Naruto as the only threat to his power, so he used a powerful spell to take away Naruto's godlike abilities. Konoha wants Naruto back to stop this tyrant. This antagonist might have an army of brainwashed ninja at his command.
Perhaps the antagonist is a group of rogue ninjas who have formed an alliance. They have developed a technique that can nullify Naruto's powers and have kidnapped him. Konoha wants him back not only because of his power but also because he is an important part of their village. The rogue ninjas plan to use Naruto's power for their own evil purposes once they figure out how to control it.
It could be an old enemy of Naruto's who has found a way to harness dark chakra and has created a powerful weapon. This enemy fears Naruto's godlike powers and has found a way to send Naruto into a deep slumber where he can't use his powers. Konoha needs to wake Naruto up and fight this enemy before the weapon is fully activated and destroys everything.