Dutch Empire/Indonesian Independence
Initial Declaration 
Two days after the Japanese surrender in August 1945, Sukarno and fellow nationalist leader, Mohammad Hatta, declared Indonesian independence. The Netherlands, only very recently freed from German occupation itself, initially lacked the means to respond, allowing Republican forces to establish de facto control over parts of the huge archipelago, particularly in Java and Sumatra. On the other hand, in the less densely populated outer islands, no effective control was established by either party, leading at times to chaotic conditions.
British Military Action 
Initially the United Kingdom sent in troops to take over from the Japanese and soon found itself in conflict with the fledgling government. British forces brought in a small Dutch military contingent which it termed the Netherlands Indies Civil Administration (NICA). When a member of the NICA raised a Dutch flag on a hotel in the country's second-largest city, Surabaya, Indonesian nationalists overran the Japanese proxies guarding the hotel and tore the blue stripe off the flag, forming the red-and-white Indonesian flag.
On November 10, 1945, Surabaya was attacked by British forces, leading to a bloody street-to-street battle. The battle for Surabaya was the bloodiest single engagement in the war and had successfully demonstrated the determination of the rag-tag nationalist forces. It also made the British reluctant to be sucked into a war it did not need, considering how outstretched their resources in southeast Asia were during the period after the Japanese surrender.
Dutch Military action 
As a consequence, the Dutch were asked to take back control, and the number of NICA forces soon increased dramatically. Initially the Netherlands negotiated with the Republic and came to an agreement at Linggarjati, in which the 'United States of Indonesia' were proclaimed, a semi-autonomous federal state keeping as its head the Queen of the Netherlands. Both sides increasingly accused each other of violating the agreement, and as consequence the hawkish forces soon won out on both sides. A major point of concern for the Dutch side was the fate of members of the Dutch minority in Indonesia, most of whom had been held under deplorable conditions in concentration camps by the Japanese. The Indonesians were accused (and guilty) of not cooperating in liberating these prisoners.
The Netherlands government then mounted a large military force to regain what it believed was rightfully its territory. The two major military campaigns that followed were declared as ere 'police actions' to downplay the extent of the operations. There were atrocities and violations of human rights in many forms by both sides in the conflict. Some 6,000 Dutch and 150,000(including civilians) Indonesians are estimated to have been killed.
Although the Dutch and their indigenous allies managed to defeat the Republican Army in almost all major engagements and during the second campaign even to arrest Sukarno himself, Indonesian forces continued to wage a major guerrilla war under the leadership of General Sudirman who had escaped the Dutch onslaught. A few months before the second Dutch offensive, communist elements within the independence movement had staged a failed coup, known as Madiun Affair, with the goal of seizing control of the republican forces.
Independence and Netherlands New Guinea 
With the United States government threatening to withdraw the Marshall Plan funds, which were vital to the Dutch rebuild after the Second World War, the Netherlands government was forced back into negotiations, and after the Round Table conference in The Hague, the Dutch finally recognised Indonesian independence on December 27, 1949. At the time, other than most of Sumatra, and small parts of Java, all of Indonesia was under Dutch control. New Guinea was the only part of the East Indies not given up. Elections were held across Dutch New Guinea in 1959 and an elected New Guinea Council officially took office on April 5, 1961, to prepare for full independence by the end of that decade. The Dutch endorsed the council's selection of a new national anthem and the Morning Star as the new national flag on December 1, 1961.
Indonesia attempted to invade the region on December 18, 1961. Following some skirmishes between Indonesian and Dutch forces an agreement was reached and the territory was placed under United Nations administration in October 1962. It was subsequently transferred to Indonesia in May 1963. The territory was formally annexed by Indonesia in 1969.