This will at first sound a lot like PMD2 but I have the whole storyline figured out and it is actually way different.
Prologue
A horrible gray fog clung to the cold cobblestone path as a dark figure moved quickly like a shadow across it. It looked around nervously then quickly slipped through a wall.
“Greetings Lord Darkrai,” it said in a feminine voice kneeling before a seventeen foot tall black dragon-like creature whose blue eyes seemed to be able to pierce through ones soul.
“Greetings Mismagius,” it said in an ancient whispery voice. “I assume the plan is coming into play? Will I have to stay in this Lugia’s body for long?”
Mismagius nodded “Yes, Arbok, Hypno, and Absol are hiding the time gears while Rhyperior and Aggron are destroying the temporal tower, and Dusknoir is making a name for himself as an explorer, just as you planned. And no you will not have use for Lugia's body much longer.” Mismagius smiled.
“Good” it said menacingly, “now for your new assignment.” Darkrai almost laughed. “You will capture the legendary pokemon, and infect them, understood”
Mismagius nodded, “Yes I understand, but what if I can’t-“
Darkrai cut her off “You will succeed, failure is not an option.” Darkrai said simply.
Mismagius nodded again, she knew what would happen if she failed, Darkrai would kill her or worse. “Yes.”
“Good, then you are dismissed,” Darkrai said coldly. As the ghostly form left the room Darkrai smiled. “It won’t be long now, even if Suicune stands in my way. What can he do? Soon I will be restored to my former power!” A horrible cackle rang through the corridor.