Indonesia's campaign of infiltrations into Borneo sought to exploit how ethnically and religiously diverse Sabah and Sarawak were compared to that of Malaya and Singapore, with the intent of unravelling the proposed state of Malaysia.

Coinciding with Sukarno announcing a 'year of dangerous living' and the 1964 race riots in Singapore, Indonesia launched an expanded campaign of operations into Peninsular Malaysia on 17 August 1964, albeit without military success.

[21] The Central Intelligence Agency (CIA), primarily through its Taiwan-based subsidiary Civil Air Transport (CAT), had been covertly providing support to rebels on remote islands, seeking to weaken, if not outright oust President Sukarno's regime.

By late 1957, the transport of weapons and ammunition to Sumatra by merchant ships and night submarines had become increasingly common, but the Americans believed that for their clandestine assistance to be truly effective, such operations required the use of British facilities in Singapore to refuel and support CAT missions launched in Bangkok, Taiwan, or the Philippines.

In May 1961, the UK and Malayan governments proposed a larger federation called Malaysia, encompassing the states of Malaya, North Borneo, Sarawak, Brunei, and Singapore.

Dense mangrove forest covering vast tidal flats intersected with numerous creeks is a feature of many coastal areas, including Brunei and either end of the border.

However, the Brunei People's Party was in favour of joining Malaysia on the condition it was unified with the three territories of northern Borneo with their own sultan, and hence was strong enough to resist domination by Malaya, Singapore, Malay administrators or Chinese merchants.

Soebandrio met with a group of their potential leaders in Bogor, and Nasution sent three trainers from Resimen Para Komando Angkatan Darat (RPKAD) Battalion 2 to Nangabadan near the Sarawak border, where there were about 300 trainees.

Sukarno accused Malaysia of being a British puppet state aimed at establishing neo-imperialism and neo-colonialism in Southeast Asia, and also at containing Indonesian ambition to be the regional hegemonic power.

However, while Sukarno made no direct claims to incorporate northern Borneo into Indonesian Kalimantan, he saw the formation of Malaysia as an obstacle to the Maphilindo, a non-political, irredentist union spanning Malaya, Philippines and Indonesia.

Indonesia argued that the establishment of Malaysia allowed the United Kingdom to maintain her unique privileges regarding the use of the Singapore base and keep close ties to British defense needs in Southeast Asia constituted an implied threat.

Subandrio, the Indonesian foreign minister, was careful to explain to American ambassador Howard P. Jones that the confrontation policy was concerned with Malaya not Malaysia and was a reaction to Malayan and British anti-Djakarta, pro-rebel activity in 1958, and promotion of program to split off Sumatra as diplomatic efforts to settle the Malaysian dispute picked up steam in the summer of 1963 through ministerial and summit level talks in Manila.

At the Manila meeting, the Philippines and Indonesia formally agreed to accept the formation of Malaysia if a majority in North Borneo and Sarawak voted for it in a referendum organised by the United Nations.

[36] However, following the conclusion of the Manila talks, the Malayan prime minister Tunku Abdul Rahman announced that the proposed Malaysian state would come into existence on 16 September 1963, apparently irrespective of the latest UN report.

[42] Meanwhile, the Indonesian armed forces led by Lieutenant General Ahmad Yani became increasingly concerned with the worsening domestic situation in Indonesia and began secretly contacting the Malaysian government, while obstructing the confrontation, reducing it to a minimal level.

[50] By the final months of 1964, the conflict once again appeared to have reached a stalemate, with Commonwealth forces having placed Indonesia's campaign of infiltrations into East Malaysia in check for the moment, and more recently, the Malaysian Peninsula.

[citation needed] However, the fragile equilibrium looked likely to change once again in December 1964 when Commonwealth intelligence began reporting a build-up of Indonesian infiltration forces in Kalimantan opposite Kuching, which suggested the possibility of an escalation in hostilities.

[51][52] Meanwhile, due to the landings in Malaysia and Indonesia's continued troop build-up, Australia and New Zealand also agreed to begin deploying combat forces to Borneo in early 1965.

[54] Given the sensitivity of these operations and the potential consequences if they were exposed, they were controlled at the highest level and conducted within strict parameters known as the "Golden Rules", while the participants were sworn to secrecy.

[57] Claret was largely successful in gaining the initiative for the Commonwealth forces before being suspended late in the war, inflicting significant casualties on the Indonesians and keeping them on the defensive on their side of the border.

The newly elected President of the Philippines, Ferdinand Marcos, was keen to ease tension and, to some extent, differed from his predecessor by not pursuing the North Sabah claim as fervently.

The ground forces were initially limited to just five British and Gurkha infantry battalions usually based in Malaya, Singapore and Hong Kong,[70] and an armoured car squadron.

[76] In the early stages of the conflict, Indonesian forces were under the command of Lieutenant General Zulkipli in Pontianak, on the coast of West Kalimantan about 200 km (120 mi) from the border.

Being undetectable meant being silent (hand signals, no rattling equipment) and 'odour free'—perfumed toiletries were forbidden (they could be detected a kilometre away by good jungle fighters), and sometimes eating food cold to prevent cooking smells.

[85] The role of the United Kingdom's Foreign Office and MI6 during the confrontation was brought to light in a series of exposés by Paul Lashmar and Oliver James in The Independent beginning in 1997 and has also been covered in journals on military and intelligence history.

To weaken the regime, the UK Foreign Office's Information Research Department (IRD) coordinated psychological operations (psyops) in concert with the British military, to spread black propaganda casting the PKI, Chinese Indonesians, and Sukarno in a bad light.

[citation needed] These efforts were coordinated from the British High Commission in Singapore, where the BBC, Associated Press, and The New York Times filed their reports on the crisis in Indonesia.

[88] One squadron of the British Army's 22 Special Air Service regiment was deployed to Borneo in early 1963 in the aftermath of the Brunei Revolt to gather information in the border area about Indonesian infiltration.

[91][92] The shortage of SAS and SBS personnel was exacerbated by the need for them in South Arabia, in many ways, a far more demanding task in challenging conditions against a cunning and aggressive opponent.

A significant number of British casualties occurred during helicopter accidents, including a Belvedere crash that killed several SAS commanders and a Foreign Office official, possibly a member of MI6.