Maybe they travel to a time before the Hidden Leaf Village was even founded. Here, they have to adapt to a more primitive and dangerous world. Naruto might struggle with not having the support system he had in his own time. Jiraiya could be in a position to teach the early ninjas some of the skills he developed over the years, which would significantly impact the future development of ninjutsu.
Another interesting plot twist could be that they travel to a time during one of the great ninja wars in the past. They could end up changing the outcome of battles they know about from history. Naruto's presence could inspire the soldiers with his never - give - up attitude, and Jiraiya could use his intelligence to outwit the enemy commanders. This would rewrite the history of the ninja world and have far - reaching consequences for their present time.
One possible plot twist could be that Naruto and Jiraiya travel back to a time when the Uchiha clan was at its peak. This would put Naruto in a position to potentially prevent the Uchiha massacre. He could use his knowledge of future events and his skills to change the course of history for the better. Jiraiya, on the other hand, could discover secrets about the Uchiha that were lost over time.