It could be that Naruto's fear is more personal. Maybe he's scared of losing his friends or not being able to protect the village. Jiraiya, covering him, provides not just physical protection but also emotional support. He shares his own experiences of fear and how he overcame them, which gives Naruto the strength and confidence to face his own fears.
One possible plot development could be that Jiraiya discovers the source of Naruto's fear is related to a new and powerful enemy. He then decides to train Naruto more intensively to face this threat. For example, he might teach Naruto a new jutsu that can be used against this feared adversary.
One possible plot development could be that Naruto's fear is related to a new and powerful enemy in the Hidden Leaf Village. Jiraiya, covering for him, might train Naruto in secret to help him overcome his fear and face this threat. For example, Jiraiya could take Naruto to a secluded place and teach him new jutsu.
Perhaps Naruto has just lost a fight against a powerful enemy and is feeling defeated. His crying is a result of his frustration and self - doubt. Jiraiya, covering him, then begins to train Naruto more intensively to help him overcome his weaknesses. Or it could be that Naruto has witnessed something truly horrifying in the ninja world, like a massacre. Jiraiya's act of covering him is the start of him guiding Naruto to understand the darker aspects of their world and how to face them bravely.
He also acts as a mentor. Jiraiya has a wealth of knowledge and experience. In this situation, he can use his wisdom to help Naruto understand and deal with his fear. He might tell Naruto stories of his own times of fear and how he coped, which can inspire Naruto.
Jiraiya is also a confidant. Naruto can trust him with his fear, and Jiraiya can keep Naruto's secrets. This relationship allows for a deeper bond between them, which could lead to Naruto opening up more about his feelings and Jiraiya being able to provide more targeted help.
One possible plot development could be that Naruto quickly masters basic chakra control under Jiraiya's strict training. This early success might make Naruto overconfident, leading to a challenge where he realizes he still has a lot to learn. For example, he might face a powerful opponent in a sparring match arranged by Jiraiya and struggle initially, teaching him the importance of continuous training.
One possible plot could be that Naruto has a major disagreement with Jiraiya over his training methods. Maybe Naruto feels that Jiraiya is being too hard on him or not focusing on the right aspects of his growth. So, in a fit of anger or determination, he decides to ditch Jiraiya and go off on his own to train in a new way.
One possible plot could be that Naruto and his friends are sent to a 'scared straight' type of program in the Hidden Leaf Village. They are shown the harsh realities of what could happen if they continue on a wrong path, like if they were to give in to the temptations of the dark side of ninja skills. This experience makes them more determined to uphold the values of their village.
Well, that's a really strange concept for a fanfiction. One possible plot could be that Jiraiya's teachings, which are often a bit off - color in the original series, accidentally go too far and make Naruto start acting inappropriately. But this would be a very dark and out - of - character take on Naruto.
One possible plot development could be that Kushina's spirit somehow manages to break through the boundaries between the afterlife and the living world. She then tries to communicate with Naruto, perhaps through dreams at first. This could lead to Naruto starting to search for a way to bring her back permanently, involving him in some sort of ancient and dangerous ritual that he discovers in some long - forgotten scroll.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.