During the scene when Mulan decides to go to war instead of her father, she decides to do it while sitting on the foot of the Great Stone Dragon.
The image of the dragon looking over Mulan is repeated several times throughout the sequence, and the bolts of lightning strike at significant times whenever the dragon is in sight. When Mulan takes her father’s scroll and when she is praying to her ancestors, the Great Stone Dragon can be seen. It is also engraved on both the sword Mulan uses to cut her hair and the handles of the wardrobe containing the armor are in the shape of the dragon’s head.
The dragon’s eyes glowing in the temple symbolizes Mulan’s role as the protector of her family awakening, instead of the actual dragon.
The reason Mushu couldn’t wake the dragon is because the dragon was no longer there. Mulan is implied to be the Great Dragon that protects her family.