During the time of 18th Da'i e Mutlaq Saiyedna 'Ali Shamsuddin bin S 'Abdullaah RA, Ja'far did Fitnat (Treason) in India and persecuted thousands of Mumineen all over Gujarat. He went to Yemen without the permission of Maulaai Hasan RA of Ahmedabad.
Stayed there for more than 3 years. Tried to win over Saiyedna 'Ali Shamsuddin RA but in vain. Saiyedna instructed him to be loyal to Maulaai Hasan RA in India. He instructed him to lead Namaaz only till Aden. He returned to India and led Namaaz without Razaa at 3 places. He dissented and did Fitnat which reached at it's peak in 850 AH. He was killed at Champaner. Even after his assassination, his followers continued to wreak havoc in Ahmedabad. His followers are known today as Ja'fari Patani Bohras.