I had an idea here and I'll write it out;
(this one is very weird so bare with me)
Out of revenge for being the main reason for hating herself, Palkia wraps the moon to a different dimension. As Palkia sits back and enjoys her suffering, Cresselia is distraught over the moon's disappearance and angrily orders her underlings to search for it. While Giratina and her friends try to help her cope through this unfortunate situation, the moon goddess feels that she should get to the bottom of the situation. Who would be so vile as to steal the moon?
So she seeks the strongest Pokemon of Unova to use her Psychic powers to align the stars and trace the moon and figure out the culprit.