Commander Woodruff: "We've got a lock on Farnsworth's location. He's sure to have something standing in the way, but get there and finish this!"
Farnsworth is a three stage battle against his final creation, a giant underwater dome/squid that houses him during the fight.
The first stage is the top of the ice berg, so to speak, as a small dome with one shielded section. Under the shield is a patch of spikes meant to charge up and shoot a beam of electricity, the only way to damage Farnsworth is to wait for him to charge his weapon. As he charges the shield dissipates allowing the patch of spikes to be shot to damage him.
Stage two is a larger dome underneath the first which raises out of the water. The idea is the same, he can only be hurt when charging, but now he has three spike patches instead of one. Once all three are destroyed stage three can begin.
Farnsworth's last resort is to bring his entire creation out of the water, it stands high overhead on its mechanical legs and swings mechanical arms to hit the players. The only way to damage Farnsworth at this point is when he drops his 'energy sacs' from his underside. There are three 'sacs' of monovisions that need to be burst before Farnsworth finally falls.