Within the Empire too was a small minority which favoured adopting Western philosophy and civilization. Thus, all Bediuzzaman's endeavour was to prove and demonstrate the falseness of these accusations, and that far from being incompatible with science and progress, the Qur'an was the source of true progress and civilization, and in addition, since this was the case, Islam would dominate the future, despite its relative decline and regression at that time.
The years up to the end of the First World War were the final decades of the Ottoman Empire and were, in the words of Bediuzzaman, the period of the 'Old Said'. In additions to his endeavours in the field of learning, he served the cause of the Empire and Islam through active involvement in social life and the public domain. In the War, he commanded the militia forces on the Caucasian Front against the invading Russians, for which he as later awarded a War Medal. To maintain the morale of his men he himself disdained to enter the trenches inspite of the constant shelling, and it was while withstanding the overwhelming assaults of the enemy that he wrote his celebrated Qur'anic commentary, Signs of Miraculousness, dictating to a scribe while on horseback. Stating that the Qur'an encompasses the sciences which make known the physical world, the commentary is an original and important work which in Bediuzzaman's words, forms a sort model for commentaries he hoped would be written in the future, which would bring together the religious and modern sciences in the way he proposed. Bediuzzaman was taken prisoner in March 1916 and held in Russia for two years before escaping in early 1918, and returning to Istanbul via Warsaw, Berlin, and Vienna.

The defeat of the Ottomans saw the end of the Empire and its dismemberment, and the occupation of Istanbul and parts of Turkey by foreign 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 Dar?'l-Hikmeti'l-Islamiye, a learned body attached to the Shaykhu'l-Islam's Office, and combatting the British, Bediuzzaman 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.' 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 which successfully countered this.

Remaining some eight months in Ankara, Bediuzzaman understood the way Mustafa Kemal and 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 combatted in the realm of politics. When offered various posts and benefits by Mustafa Kemal, he 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.