Shortly, Muslims and Croatians wanted to secede from YU. Alternatively, Croatians wanted to join Croatia. Serbians wanted to remain in YU alongside other Serbians.

War had its background in WW2 as there were many crimes commited by Muslims and Croatian militias, aided by Germans and partialy Italians, aganst Serbs. I recommend googling about massacres against Serbs in Croatia and Bosnia during WW2. Communism managed to hold these tensions and put them under the carpet, but with economic crises rising in the 80s and emergence of new members of Communist party in all three nations, which were far right - winged, nationalistic feelings started to boil. People were encouraged to hate other nationalities and, in case of Serbs, massacres in WW2 were especially pointed out.

After independence referendum boycotted by Serbians, Bosnia declared independence. Bosnian Serbs rose to arms already provided by the retreating federal army (plus many male citizens from all three nations were part of reserve force from time of big YU period, so they had military training). What happened after was basicaly making ethnicly cleansed land for its own population and it was done by all three sides. Who was more powerful or more concentrated got their hands on that particular area: in case of Muslims, central Bosnia and Sarajevo, in case of Serbs, eastern, northern and western Bosnia, in case of Croats, southwestern parts.