I know Avalanche already answered this but I spent all this time typing this thing (even though it's probably TMI) so I'm going to post it anyway.
In the second part there are four cranes, one in each corner of the room. Walk up to a crane and you get to control it. Mata Hairy (the NPC "leading" the CFO) will give you some quick instructions before the second part begins. Basically, someone has to disable the goons (coming out of the CFO's undercarriage) for each craner. Once a goon is disabled you can move the magnet on the crane using the arrow keys, then when you're close enough to a goon you can press the control key to activate the magnet and pick it up. Then pull the magnet all the way back and push it forward again to get enough momentum to throw it at the CFO. When you get a hit it will show in red numbers above the CFO's head. If the hit is strong enough the CFO will be stunned, then you can try throwing a safe. Pick up a safe the same way as a goon, but only throw a safe when the CFO is stunned, or else the CFO will gain the safe as a helmet and you will be unable to throw any goons at the CFO until you knock the helmet off with another safe.
At first you may want to stick to stomping, since craning can be overwhelming and you may want to leave it to the more experienced toons. The goons are disabled just like Avalanche said, and it often works best if every stomper picks a craner to protect, as opposed to running around stomping random goons. There's a timer on the run and as time goes on the goons will get bigger (started at tiny yellow-hatted ones and ending with big red-hatted ones that do a lot of damage). When you disable a goon a treasure will come out (just like the toon-up ones in the playground) and you can run through it to gain laff. Smaller goons give smaller toon-ups. The light on the CFO's chest goes through the same stages as a regular cog and when he finally runs out of hit points you've defeated him. Depending on the abilities of the craners and the stompers this may happen very quickly, or not at all.
So, in a nutshell, that's it. If you have any questions or I left anything out please feel free to ask.
