Suharto dies in a car crash somewhere in the 1963-1964 range. I personally believe the coup was his doing so I'm going at it from that frame of reference.
With Suharto dead the coup obviously doesn't happen. Indonesia continues in its state of affairs directly pre-coup with simmering tensions between the main constituencies in the country (Communists, the military, nationalists, and Islamists) remaining in conflict and Sukarno on top. The plan to create an armed peasant militia is enacted (I think Sukarno was leaning that way pre-coup), and creates a force of hundreds of thousands of armed PKI members (primarily). Interesting note: forming the peasant force was actually supported by the Navy and Air Force but not by the Army.
At some point there is an actual Communist coup led by mid and low-level officers who are PKI members. The PKI wins with the support of part of the military, the peasant militia, and the enthusiastic support of the Soviet Union. The Navy and Air Force grudgingly join in when it becomes clear the PKI will probably win. They may not be Communists themselves but are somewhat sympathetic to the left as shown by the fact that they supported creating the PKI militia and they don't want to be on the losing side.
Internally the new overlords either launch a spectacular genocidal cleansing of all Islamists, right-wing nationalists, and military members suspected of being disloyal or neutralize the most threatening elements while bringing the rest into line. Under Aidit, disastrous agricultural reorganizations, human rights abuses, industrial reorganizations for the purpose of boosting military capability at the expense of everything else, and the other typical parts of being a Communist dictatorship follow.
Konfrontasi with Malaysia and the Commonwealth is aggressively stepped up, possibly with actual wars occurring. It could be an Arabs-Israel thing where every six or so years there's a new war, with Jakarta trying to break the new federation. That could produce some interesting TL's. They would probably find a way to mess around in Papua New Guinea, too. In a place with that much tribal conflict there's going to be plenty of potential proxies.
The effects on the Indonesian military would be quite interesting. I suspect that they would go the route of Britain and to an extent Imperial Japan and have the Navy be the senior service. Island nations generally do that. They got quite a lot of naval aid from the USSR under Sukarno in OTL, including a
cruiser.
For absolute maximum bonus points have this result in the
Project 1153 OREL actually getting built. Brezhnev vetoed it because of the expense and because aircraft carriers were not seen as part of the Communist military vision. In their minds they were imperialist tools. Indonesia could change that by providing an example of a good Communist country that was also a naval and seafaring power. Add that to the Indonesians offering to enter the program and chip in part of the cost (say a quarter) in exchange for some hulls and you're golden.