Gunyolk...
Mario, Geno and Toadstool can dethrone the Factory Chief and bust Gunyolk. Use the Geno Flash and Blast a few times, as well as regular attacks. Alternate your focus between Gunyolk and the Chief. Once the Chief's gone, kick Gunyolk's metal buttocks while it's down. Whenever it uses the Breaker Beam, have Toadstool Group Hug everyone before she does anything else. By the way, if you need any advice on the Clerk, Manager or Director, this is all I think you need: Geno and Toadstool for the Clerk, Mallow and Toadstool for the Manager, and Bowser and (you guessed it) Toadstool for the Director.