Nichiren identified reason or theory (ri) with the shakumon, and substance or practice (ji) with the hommon. In other words, the first fourteen chapters were to him mere abstract teaching, while the last fourteen chapters constituted for him the concrete teaching. According to him, ri or abstract teaching was congenial with the Tendai School, while ji or concrete teaching was appropriate to the Nichiren School. This identification of shakumon with ri and of hommon with ji is another instance where Nichiren’s teaching differs from Tendai Daishi’s teaching. Though both agreed on the division of the sūtra into shakumon and hommon, Tendai Daishi emphasized the identical nature of both parts. He maintained that the Ten Mysteries of each coincided; that both parts contained the Three Dharmas, in which the Law of the Living Beings was the standard for shakumon, and the Law of the Buddha the standard for hommon. He says textually: “Notwithstanding hon and shaku being different, they are the same in being incomprehensible.” Incomprehensible (fushigi) is to be here understood as wonderful or mysterious (myō), i.e. transcending all relative understanding and mental capacity.

Nichiren opposed these theses, restating his belief that shakumon, instead of being identical with hommon, was inferior to it. In the fivefold “Classification of the Five Gradual Contrasts” (Go-jū sō-tai), the Contrast of Origin and Trace is the fourth of five contrasts. Here the Origin (hon) is the fundamental teaching of the Hoke-kyō, while the Trace (shaku) is that which is not considered as fundamental. In his Jippōkai ji, Nichiren further condenses the evolution of Buddhism into four stages:

1. ni zen—teaching before Hokke
2. shakutnon—teaching of Trace
3. hommon—teaching of Origin
4. kanjin—meditation on mind

Thus the whole teaching by Śākyamuni proceeds from shallow to deeper and deeper levels: Nichiren says in this book: “When the great teaching of shakumon arises, then the teachings before it perish. When the great teaching of hommon arises, then shakumon and the teachings before it perish. When the great teaching of kanjin arises, then all hon and shaku and all teachings before it perish.” The real meaning of hommon appears therefore in kanjin, in intuition. It is this hommon of higher potence which Nichiren calls “the great white doctrine among the great white doctrines”, “the mystical medicine among the mystical medicines.”