Perhaps in the fanfic, they travel to a time when the Uchiha clan was still intact. Naruto and Yoshina could try to prevent the Uchiha massacre. This would be a huge change in the Naruto story. Naruto, with his knowledge of the future, could try to bridge the gap between the Uchiha and the rest of the village. Yoshina could use her special skills to uncover the real mastermind behind the plot against the Uchiha, if there is one other than Danzo. This would create a whole new set of relationships and story arcs.
One interesting plot could be that Naruto and Yoshina time travel to the era of the Sage of Six Paths. They could learn about the origin of chakra directly from the source. Naruto might gain new powers or a deeper understanding of his own abilities. Yoshina could also have her own revelations. Another plot could be that they are sent back to when Naruto was a child and they have to prevent Orochimaru from infiltrating the village earlier. This would change the power dynamics in the village and Naruto's growth path.