Gould discusses how the conflicts between science and the humanities (religion) are fabricated to put an illogical conflict that should not exist and only drags down both. Instead, science and the humanities should learn to work together. The humanities pride themselves on having one single tactic that works (the method of the hedgehog) while the sciences pride themselves on having a variety of tactics that work (the method of the fox) and that both should learn from each other in order to propel their respective studies into the future. The Magister's Pox was the method of creating the conflict so that they could remain in control.
Interesting tidbit: Gould argues an unusual point for a scientist: that the perfection of the earth and the biosphere should do more to prove that there is a God than anything short of actually seeing Him. Evolution has one of two possibilities: that nature figured out how to do things be its self or that God put things into such a perfect organization and alignment that He did not need to continually intervene.