A brief history of Bahasa Indonesia:
Malay, in some form, has been a major language of the Indonesian archipelago and the adjacent mainland for over a millennium. During this time, Hindu empires rose and fell, Islam became the dominant religion, and English, Dutch, and Portuguese colonies were establish. It contains many loanwords from Sanskrit and its descendants, from Arabic, and from the European languages.
In the early 20th century, Malay remained the major language of a region divided between the Dutch East Indies and British Malaya. By this stage, the use of the Latin script for Malay in either territory had become dominant. There were differences between the formal Malay of these two areas, and considerable differences among the various dialects _within_ the two areas. The Dutch East Indies housed speakers of countless other languages: some of them closely or distantly related to Malay, some not.
In the 1920s, leaders of the independence movement of the Dutch East Indies chose a particular formal variety of Malay as the basis of the official language of a country that did not yet exist: Indonesia. This was Classical Malay, a dialect that had been previously used in the courts of the Malaccan Sultanate. Bahasa Indonesia was a standardised, simplified version of this Classical Malay, written in the Latin script with orthographic rules that reflected a Dutch influence. For instance, the digraphs oe and sj were used. At the point that this decision was made, it is probably fair to say that technically there were no native speakers of Bahasa Indonesia: no one had been raised using quite that form of Malay, ever, though some spoke dialects that were similar.
By the 1930s, independence-minded political leaders were insisting on the use of BI for their official communications. Independence was obtain from a war weary Netherlands in 1945, and so this national language finally had an actual nation of which to be the language. Its use as a second language grew rapidly in the 1950s and 1960s as it was taught, along with the local language, in schools from one end of the country to the other.
In the 1970s, Indonesian spelling was reformed to make it more similar to Bahasa Melayu, the national language of Malaysia: oe became u, sj became sy, dj became j etc.
Today, the use of BI in official broadcasts or documents is near universal. Some 10% of the language identify Bahasa Indonesia as their native tongue. Different sources give different estimates, but roughly 60% of the population speak BI fluently as a second language, and 95% speak it to some level. I would guess that the other 5% either completed most of their schooling before the 1960s, or are in remote areas of Papua, Borneo or Sulawesi.