After completing the Spirit's Grave and returning to the Maku Tree, you will be directed to Crescent Island to find Nayru. This journey will eventually lead you to acquire the Harp of Ages, a magical instrument that allows Link to travel between the past and present versions of Labrynna. This mechanic is central to solving many of the game's puzzles and progressing the story.
The Harp of Ages is obtained after a series of events involving Nayru and Veran. Once you have it, pressing the Select button will bring up a menu where you can choose which tune to play. Initially, you'll only have the 'Tune of Echoes,' which allows you to travel between the present and past at specific time portals. As you progress, you'll learn more tunes that have different effects, such as warping to dungeons or changing the season.