Willan made further interviews with other Malay rulers over the next few days, and made assessments of the political situation in each state. His studies were forwarded to the military administration, and Sir Harold MacMichael, the former high commissioner of Palestine was empowered to sign official treaties with the Malay rulers over the Malayan Union proposal scheme. MacMichael made several visits to the Malay rulers, beginning with Sultan Ibrahim in October 1945. The Sultan quickly consented to MacMichael's proposal scheme, which was motivated by his strong desire to visit England at the end of the year. MacMichael paid further visits to other Malay rulers over the proposal, and sought their consent over the proposal scheme. Many Malay rulers expressed strong reluctance in signing the treaties with MacMichael, partly because they feared losing their royal status and the prospect of their states falling into Thai political influence.
The treaties provided that United Kingdom had full administrative powers over the Malay states except in areas pertaining to Islamic customs. The Malays strongly protested against the treaties, as the treaties had the effect of circumscribing the spiritual and moral authority of the Malay rulers, which the Malays held high esteem over it. Communal tensions between the Malays and Chinese were high, and the prospect of granting citizenship to non-Malays was deemed unacceptable to the Malays. In particular, politicians in Johor were extremely unhappy with the willingness of Sultan Ibrahim to sign the treaties with MacMichael, and voiced out that the Sultan Ibrahim had violated the terms in the Johor state constitution which explicitly forbade any foreign powers to assume legitimate control over the state. In early February 1946, seven political dissidents led by Awang bin Hassan organised a rally to protest against the Sultan's decision for signing the treaties, and Onn Jaafar, who was then serving as a district officer in Batu Pahat, was invited to attend the rally.
The rally was held on 1 February 1946 at the Sultan Abu Bakar State Mosque, and protesters shouted nationalistic slogans and called for the dethronement of Sultan Ibrahim. Malay nationalistic slogans were raised during the rally, many of whom were directed against the Sultan himself, whom they accused him for committing treason against the Malay race by signing the treaties. News of the rally reached the Sultan Ibrahim on 22 February, who was then residing at Grosvenor House in London. Sultan Ibrahim approached the colonial office and expressed his withdrawal of support for the proposal scheme, but this did not appease the political dissidents and Onn continued to organise more rallies in the other Malay states to muster further support for his calls against the Malayan Union, and formed United Malays National Organisation (UMNO) in May.
Sultan Ibrahim returned to Johor in early September 1947 and attended UMNO's second general meeting at Istana Besar, which was led by its youth chief, Hussein Onn. Although many Johor politicians still held a critical opinion of Sultan Ibrahim over the treaties with MacMichael, the UMNO delegates gave him a rousing welcome when he arrived at the palace. Critical opinions against the Sultan waned after the Federation of Malaya was established the following January, which restored the rulers' powers. Shortly before Sultan Ibrahim left for England in May, he personally donated a lump of $5,000 to UMNO, hoping to improve relations with UMNO leaders and Onn himself, who was appointed the Menteri Besar of Johor in 1946.