The UNSC decides to deploy their most powerful weapon: the NOVA bomb. A weapon with enough yield to crack a planet in half.
Thats nice, except all of the SupCom races control hundreds of planets with thousands of ACUs, each capable of creating a ground army that can brush aside any planetary defense the UNSC or Covenant have; several could probably fight the flood to a standstill. Also they can teleport these ACUs to any planet they wish, so if such a Nova bomb were to be used, it would probably have to be used on the UNSCs own planets as the SupCom races would attack first. Also as mentioned Black Sun can destroy entire planets, but I don't want to turn this into a war of super weapons.
And Tasunke, it becomes really hard to compare SupCom, where space forces are obsolete, to the Covenant navy, as neither are really able to encage eachother. Both can teleport to eachothers planets, destroy them, and then return to their own to rebuild, and do it over again almost infidintely. It just turns into a no win situation for both of them.