I recently had the chance to have a few long conversations with a podiatrist that is pretty famous in my area of Grand Rapids, MI. He long ago quit doing surgeries in favor of adjusting the bones of the feet to provide "long lasting relief."
He said it came from doing "to many surgeries for a bunion or neuroma and seeing it come back a few years later."
His explanation for how he thinks a neuroma develops is one of the best I've heard. My personal understanding was that the common neuroma between the 3rd and 4th digit of the metatarsal was from the compression that happened from a tight toe box in a shoe. He extrapolated on this concept.
When the cuboid bone becomes misaligned, the foot on impact can no longer lock the lateral line of the foot for stability on impact. This allows for the foot to actually increase the degree of pronation that occurs. Now, because of this the metatarsal bones rotate. The lateral 2 rotate laterally, the medial three rotate medially. With this the plantar nerve is put under quite a stretch, thus irritating it.
Your body has an ingenious way of protecting itself. It grows a protective coating. Picture, scraping your hand every day. What happens? A callous forms. Irritate the plantar nerve with each step, a callous will start to form around that structure. You get a Morton's Neuroma.