It could be that Naruto is scared due to some internal conflict within himself, like his struggle with the Nine - Tails' power getting out of control. Jiraiya, covering for him, would then focus on helping Naruto gain better control. He might use his own knowledge of sealing techniques and his experience with Orochimaru's cursed seal to guide Naruto.
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 is scared because of a premonition he has. Jiraiya, being the experienced ninja he is, decides to investigate the matter while keeping Naruto's fear a secret from others. He could start by looking into ancient scrolls or consulting with other wise ninjas in the village to figure out what Naruto's premonition might mean.
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.
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.
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.
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.
One possibility is that Naruto's friends launch a rescue mission. They would use their unique skills, like Sasuke's Sharingan or Sakura's medical ninjutsu combined with her combat skills, to find and save Naruto.
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.
It could also be due to a misunderstanding. Perhaps there is some misinformation spread about Sasuke in the fanfiction, like false rumors that he has a hidden and malevolent plan. Naruto, being someone who values their friendship deeply, would be scared at the thought of Sasuke turning into an enemy because of these untrue stories.
One possible plot development could be that Sakura's tears somehow give her a newfound strength or resolve. Maybe she decides to train harder to protect Naruto in the future. For example, she could seek out a powerful teacher or a hidden jutsu to become stronger.
In a fanfiction where Naruto is sealed away, there could be a focus on the emotional turmoil of his friends and family. Hinata, for example, might be extremely distraught and use her Byakugan in new ways to try and find Naruto. Sasuke could also return to the Leaf Village out of loyalty to Naruto and join the efforts to unseal him. The story could also explore how the younger generation of ninjas, inspired by Naruto's legacy, strive to become stronger to free him.
One possible plot development could be that Naruto gains a whole new level of power and is able to see and understand the world in a different way. He might be able to use the Rinnegan's abilities to finally bring true peace to the ninja world. For example, he could use the power of the Rinnegan to better understand the motives of his enemies and find non - violent solutions to conflicts.