My guess is that she's going to blow up the Sept (and maybe a large part of the city).
She's going to kill Tommen in the process.
Margery will survive, and announce she's preggers; and thus will be Queen Regent until her child is old enough to be king.
Jaime will either know she's the one who did it early on, and kill her...or more likely, when she's feeling vulnerable she'll reveal to him that she was the one who ordered the Wildfire that killed Tommen, and he'll kill her there.