They could form an alliance when a powerful enemy targets both of them. Naruto would initially be hesitant but realizes Kaguya's power could be useful. They would start to understand each other during their battles against the common foe.
Perhaps the alliance between Naruto and Kaguya would shock the entire ninja world. People would be suspicious at first, but as they see them working together for the greater good, they start to accept it. Their combined efforts could also lead to a new era of peace and understanding between different ninja clans, as they are symbols of two very different but powerful forces coming together.