The Muslim Brotherhood in Egypt announced their stance towards the issue of Sudan's union with Egypt. They sent a message to Ismail al-Azhari, stating that the Sadqi project would not achieve the aspirations of the people of the Nile Valley. The message stipulated that the correct path required the abolition of the condominium rule, and then the position of the Azhari would become clear. They expressed their complete rejection of this issue and stated that the union, in their opinion, should be based on equality and brotherhood.

The Sudanese Islamic movement in its first phase relied on the influx of a current from Egypt in the name of the Muslim Brotherhood, proposing a comprehensive development of religion and the religious establishment based on the purification of members and the organization of ranks.

A Sudanese current of Islamic orientation emerged, its origin stemming from the prevalence of communist ideas among students. This Sudanese student initiative was the Islamic Movement, formed in the late 1940s. The connection of the Islamic movement to the Muslim Brotherhood in Egypt was more intellectual and ideological than direct membership. This was followed, in the course of the formation of the Islamic movement in Sudan, by a dispute between the Sudanese student-originated movement and the popular movement.

The early stage of relations between the Muslim Brotherhood in Sudan and the Muslim Brotherhood in Egypt was spontaneous, with the Sudanese Brotherhood looking to the Egyptian Brotherhood as their brethren. The second stage involved an awareness of the relationship between the two parties. The third stage was one of disagreement, as the Egyptian Brotherhood wanted the Islamic organizations in various countries to act as subordinate peoples directly under the leadership in Egypt. They demanded that the Sudanese Brotherhood members and students pledge allegiance to the Egyptian Brotherhood, which implied complete organizational subordination. This led to a rift between the Islamic movement in Sudan and the Brotherhood and its leadership. Another group was founded, which the Egyptian Brotherhood recognized. Thus, after complete intellectual alignment, the Islamic movement in Sudan took a path far from Egypt.