BY THE GOURDS!
PMD: The Black Box
A large and powerful group of Pokemon had begun attacking several towns. Several legendaries had tried to defeat the group, but most of them refused to work together. All of the legendaries had fallen for this reason. Every town the marauders had challenged, all of them had fell. On the last town and at the final chance the legendaries had to stop the group from ruling, they finally settled their differences and grouped together.
They were slowly defeated, one by one, until all of the legendaries had fallen.
Celebi, using the last of it's strength, made a box that would be eventually be known as The Black Box. According to mythology, a team rebels had found this box and opened it. When they opened it, they went back in time, back into the time of peace. Their memories intact, they understood what they could now do in order to stop the raiders' rule. They trained, months in advance of the attack, and defeated the army on the town's final stand, which had previously failed.
It's not finished yet, since I still have to figure out how the Black Box would tie into the story. Any help would be appreciated.