Shijima is a Reason, a powerful inner philosophy that encompasses a set of natural laws, based on stillness and oneness, influenced by Buddhism and the concept of Nirvana. It is a world of perfect harmony, where there is no 'self' whatsoever, and no passion to cause dissent, conflict and destruction. Individuality is eradicated, and replaced with a collective inner peace where everyone is equal to a god, all working together as cogs in the giant, stable machine that is the Universe. This Reason is most closely associated with the Law alignment of previous Shin Megami Tensei games.
His dream is a world of silence, where the dangerous passion of man is neutralized, and everyone is at one with the world: this, he calls the Reason of Shijima.
Yosuga is a Reason, a powerful inner philosophy that encompasses a set of natural laws, based on elitism and survival of the fittest, where only the chosen elite would possess the right to live. The useless and weak elements of society would be purged from the world, leaving only the powerful and strong. Power is acknowledged as being the only thing of true worth, and only the strongest of the strongest would have the right to rule. This Reason is most closely associated with the Chaos alignment of previous Shin Megami Tensei games.
Calling the previous world too cluttered and full of unnecessary things, she resolves to create a simple, primal world where the strong reign supreme and the weak are disposed of. Thus, she establishes the Reason of Yosuga.