They are working with Caesar's Legion , and the grand plan ( You learn later is Caesar's Plan ) , is for them to attack the strip from inside helping Caesar's Legion.
I maybe wrong but this is what i understand when i talk to Caesar about the Omertas.
They're working with the Legion. If you don't stop them, then at the battle of Hoover Dam they chlorine bomb the strip.
Indeed, If you had the 80 point speech check, you can have one of the bosses tell you their plan when you're in the room that the showdown happens in. They also had a giant stockpile of guns in their basemant for their goons to mop up the strip with and then run the whole strip alone.