So I had a thought: Mimi actually dies in her sleep after many years of dealing with the nightmares Darkrai has given her--- When her time came though, Darkrai didn't seem to notice Mimi waking up for 1-2 hours early like she used to. Picking the lifeless Shaymin up, he realizes he accidentally killed her.
He knew it would happen at some point but didn't want to turn Mimi down for being so loving towards him. She's done a lot for him..
Great thought 10/10