Well, a plot could involve Naruto and Mikoto time - traveling to a crucial moment in Uchiha history, like the first Uchiha - Senju conflict. Naruto's out - of - time skills and his never - give - up attitude might change the course of that battle. Mikoto could be in a moral dilemma as she has to choose between her loyalty to the Uchiha and the greater good that Naruto is trying to achieve. Also, they could travel to a time when the Sharingan was first discovered. Naruto might accidentally affect the way the Sharingan develops in the Uchiha lineage.
One plot idea could be that Naruto and Mikoto travel back to the time when the Uchiha clan was at its peak. Naruto, with his future knowledge, tries to prevent the Uchiha massacre. He might use his skills to gain the trust of the Uchiha clan, and Mikoto, being an Uchiha herself, could help him understand the clan's culture and politics better. Another idea is that they travel to a time before the founding of Konoha. They could witness the events that led to the formation of the village and even influence those events in a positive way for the future of the ninja world.