At the end of Burning Tides, we see Bilgewater is embroiled in chaos. With Gangplank apparently gone, all the different gangs and crime lords are turning on one another. Miss Fortune seems to think that if she can get the heads of those who followed Gangplank, everything will magically be right again.
The problem with all this is that as ruthless, brutal and cruel as Gangplank might have been, he did something important: He kept Bilgewater united. And now that it's being consumed by in-fighting, Noxus will undoubtedly come in to take over. By removing Gangplank from the equation, Miss Fortune essentially opened the gate to Noxus.