Jiraiya might comfort Naruto by sharing his own experiences. He could tell Naruto about the times he faced difficulties and how he overcame them. For example, he might talk about his training with the toads and how he grew stronger through perseverance.
He might miss out on some crucial training. Jiraiya has a lot of knowledge and skills to pass on, and by running away, Naruto could fall behind in his development as a ninja.
One possible reason could be that Naruto might be afraid of the intense training Jiraiya has in store for him. Jiraiya is known for his strict and grueling training methods, and Naruto, being young and sometimes impatient, might just want to escape that for a while.
Well, one possibility is that Naruto has some kind of premonition in the fanfiction. So he quickly rushes to Jiraiya's location where Pein is attacking. And he uses his shadow clones cleverly, distracting Pein long enough to rescue Jiraiya. He could also have some secret help from a new ally or an unexpected power boost from within himself.
Their relationship would be very strong. Jiraiya would see Naruto as not just a student, but also as a connection to Minato. He would be strict but also very affectionate. Naruto would look up to Jiraiya as a father figure, since he never really had one. They would share many adventures together, with Jiraiya teaching Naruto about life, love, and ninjutsu.
It can create a sense of growth for Naruto. Without Jiraiya by his side, he has to rely more on his own instincts and the skills he has already acquired. This can lead to new character development as he faces challenges alone.
Jiraiya's reaction might be complex. He might be in awe of Naruto's new power but also sad about his departure. He could see it as a natural progression in Naruto's journey, yet still feel a pang of loneliness. He might start to reflect on his own life and training methods, wondering if he could have done something differently to keep Naruto with him. At the same time, he would be eager to see what Naruto will achieve in the world with his newfound abilities.
They often make him seem irresponsible. For example, in normal Naruto story, Jiraiya is seen as a mentor to Naruto. But in bashing fanfiction, he may be shown as being more interested in his own adventures and leaving Naruto alone at crucial times.
In the original storyline, Naruto had a deep respect and love for Jiraiya. Jiraiya was like a father figure to him, training him and imparting important life lessons. Tsunade also cared for Naruto and was an important figure in the village. In the fanfiction where Naruto hates them, it completely flips this dynamic, which is a major deviation.
In the original story, Naruto respects and looks up to Jiraiya as his mentor. He also has a good relationship with Tsunade. But in this fanfiction, the hatred is a complete departure. It changes the whole dynamic of their interactions.