The defeat of the Ottomans saw the end of the Empire and its dismemberment, and the occupation of Istanbul and parts of Turkey by imperialist forces. These bitter years saw also the transformation of the Old Said into the New Said, the second main period of Bediuzzaman's life. Despite the acclaim he received and services he performed as a member of the Darü'l-Hikmeti'l-İslâmiye, a learned body attached to the Shaykh al-Islam's Office, and combating the occupying forces, he underwent a profound mental and spiritual change in the process of which he turned his back on the world. Realizing the inadequacy of the "human" science and philosophy he had studied as a means of reaching the truth, he took the revealed Qur'an as his "sole guide;" that is, he recognized revelation over reason. In recognition of his services to the Independence Struggle, Bediuzzaman was invited to Ankara by Mustafa Kemal, but on arrival there, found that at the very time of the victory of the Turks and Islam, atheistic ideas were being propagated among the deputies and officials, and many were lax in performing their religious duties. He published various works to counter this development.

Remaining some eight months in Ankara, he perceived the way the new leaders were going to take and on the one hand that he could not work alongside them, and on the other that they were not to be opposed in the realm of politics. When offered various posts and benefits he therefore declined them and left Ankara for Van, where he withdrew into a life of worship and contemplation; he was seeking the best way to proceed.

Within a short time, Bediuzzaman's fears about the new regime began to be realized: the first steps were taken towards secularization and reducing the power of Islam within the state, and even its eradication from Turkish life. In early 1925 there was a rebellion in the east in which he played no part, but as a consequence of which was sent into exile in western Anatolia along with many hundreds of others. Thus unjustly began twenty-five years of exile, imprisonment, and unlawful oppression for Bediuzzaman. He was sent to Barla, a tiny village in the mountains of Isparta Province. However, the attempt to entirely isolate and silence him had the reverse effect, for he was both prepared and uniquely qualified to face the new challenge: these years saw the writing of the Risale-i Nur, which silently spread and took root, combating in the most constructive way the attempt to uproot Islam, and the unbelief and materialist philosophy it was hoped to instil in the Muslim people of Turkey.