I really don't want to intrude on what Wily plans.
Okay then, a bit of elaboration:
[spoiler]This "something" is "The Hideout" or how it should be properly called The Flying Fortress - Azavaron. That's where Josei, Akai and Kharaxel were lead by Sala to find Mr. Wildgun (it happened quite recently). Tron who was in Kharaxel's body, is aware of its existence now, and he's going to capture Sala, beat her up and take the True Adventurers Card, which will allow him to enter Azavaron and then take it over.
Then he's going to contact The Resistance and tell them to try and stop him from dropping the city on the world.
Of course, it will never fall. Because depending on the situation and how everything evolves, Tron will be defeated and the city will resume its flight.
Basically, what I had in miind is having the Resistance get onto the city with the help of Wildgun, kill Tron and then stop the city from falling by basically "hitting special kinds of brakes".
I also think, Wily would like to help stop this, since hey, if the world suffers damage from the hit then he won't be happy. Being a mad scientist hell bent on WORLD DOMINATION.
[/spoiler]
But welp. As I said, I can always think of something else.