On the 30th of August 1999 the people in East Timor went to the polls under the watchful eyes of UNAMET to decide on East Timor's future. They overwhelmingly chose independence from Indonesia.
The decision of independence immediately lead to Indonesian trained and supplied militias killing approximately 1500 people. Indonesia troops and the militias forced almost 200,000 people into West Timor causing a refugee crisis and destroyed East Timorese infrastructure.
The violence quickly lead to Australia gaining a UN resolution to authorise an Australian lead peacekeeping force to East Timor. Australian leaders were so worried this might lead to a war with Indonesia they forward deployed F/A-18s and F-111s to RAAF Tindal. 1st Armoured Regiment (with Leopard 1s), 105mm guns and 155mm guns were moved to Darwin and readied for combat operations. 3rd/4th and 2nd Cavalry Regiment and thousands of infantry troops from several nations were actually deployed to East Timor. A US Marine battalion with organic artillery and armour was moved to the Timor Sea and placed on standby.
Thankfully, none of this was needed. Besides the final "fuck you" to East Timor in the form of destroying as much as they could on the way out the Indonesian military left mostly peacefully and the militias fled over the border into West Timor. But what if they hadn't?
Looking at news from the time it seriously looked like the Indonesian were prepared to fight over this. Many Indonesian didn't think it was actually possible East Timor would vote for independence let alone with such a large margin and believed it to be a UN conspiracy to undermine their nation.
What would need to change for this to happen? How would such a war go? How far would INTERFET go? Would they stop at the new border or would they push further (such as taking the whole island) to create a buffer zone? What sort of troop deployment from Australia, the US and allies would this require?