The Kingdom of Sarawak was an independent state that was a British protected state–Britain handled defence and foreign affairs–until 1946 when the ruling monarch ceded the country to the UK as a crown colony due to his belief that it didn't have the resources to rebuild after the Second World War and Japanese occupation plus having fallen out with his nephew who was heir apparent. This wasn't very popular with the locals resulting in large protests but they were ignored. In 1963 it, along with the crown colony of North Borneo – which had absorbed the crown colony of Labuan in 1946, was joined with crown colony of Singapore and the Federation of Malaya to form Malaysia.
So what happens if Charles Vyner Brooke as Rajah decides not to cede his kingdom to Britain, or having slightly better relations with his nephew Anthony Walter Dayrell Brooke abdicates in his favour? In our timeline it made sense to join Sarawak and North Borneo to Malaya since it was the main British territory in the region, here though with an independent Sarawak you have it and Brunei sitting between Malaya and North Borneo. The three main options I can see are: North Borneo still becomes a part of Malaysia, it becomes an independent country, it's joined with the Kingdom of Sarawak.
So what happens if Charles Vyner Brooke as Rajah decides not to cede his kingdom to Britain, or having slightly better relations with his nephew Anthony Walter Dayrell Brooke abdicates in his favour? In our timeline it made sense to join Sarawak and North Borneo to Malaya since it was the main British territory in the region, here though with an independent Sarawak you have it and Brunei sitting between Malaya and North Borneo. The three main options I can see are: North Borneo still becomes a part of Malaysia, it becomes an independent country, it's joined with the Kingdom of Sarawak.