The Crystal Challenges are 5 platforming challenges introduced in the Strife and Ruin DLC. Each challenge gets progressively harder and must be completed within the designated timer window or else the progress resets. The portals to access them appear throughout the map behind breakable walls. However, the portals are not linked to any specific course. Instead, each course must be completed in the specified order.
The purpose is to retrieve the shard of crystal at the end of each level to help Miriam return to her world. When you complete the challenges and return to All the Tears of the Sea, you will receive the Cantiña of the Blue Rose prayer.