One interesting plot twist could be that when Naruto and Mito time travel, they accidentally change a major event in the Uzumaki clan's history. For example, they prevent the destruction of a powerful Uzumaki artifact that was originally lost. This could then lead to a whole new power dynamic in the Naruto universe, as other villages might try to steal or ally with the Uzumaki clan for this newfound power.
A really cool plot twist could be that the time travel itself was a setup by an unknown enemy. Naruto and Mito find out that they were lured into the past to be used as pawns in a much larger scheme. This enemy could be trying to use their combined powers to open a portal to a different dimension or revive an ancient and dangerous force. As they discover this, they have to find a way to outwit the enemy while also dealing with the changes they've already made to the past.