In some Naruto clock tower fanfiction, antagonists can also be main characters in a sense. For example, a powerful and mysterious ninja who wants to destroy the clock tower to disrupt the village's balance. Naruto has to face this antagonist, and in the process, we learn more about the clock tower's importance not just to the village but to the entire ninja world.
Often, there are original characters created by the fanfiction authors. These characters could be new ninjas in the village who have a special connection to the clock tower. For instance, a young ninja who has the ability to hear the clock tower's 'voice' and believes it holds the key to a great power. Naruto then teams up with this character to explore the secrets of the clock tower.