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The small island nation of Tidore seems like it starts in a terrible position, but actually doesn't and with patience and a good start can become a real trade power in the Mollucas and Indonesia later in the game.
The first thing that Tidore should do is to rival and fabricate a claim on Ternate, to the North. It is advisable to continue building up your spy network as it increases your siege ability. They are just as wealthy as Tidore – both provinces have 5 tax, 5 production and 3 manpower. The player should attack Ternate as soon as possible and should not refrain from using mercenaries. Instead of fighting with separatists the player may find it easier to simply increase autonomy in Ternate. The next recommended target is Makassar. The player is not able to fabricate claims on them and so should instead try sending light ships on protect trade mission (therefore it is not worth to dispose of ships) to increase trade share to 10%, and then justify trade conflict using diplomacy unless the player wants to declare a no-CB war (highly advised against). While MakassarMakassar may lie within the reach of Tidore's lands to be cored, it should be vassalized instead. It is very likely that the new subject already has some claims on some of its Sulawesi neighbours – they can be attacked using vassal casus belli, but annexed in the peace deal by the player instead and cored, since they lie in a colonial range. From there next targets can be claimed on in a regular way. Makassar Should be annexed as soon as the player has used these claims.
Tidore starts out a Animist, changing to Sunni or Hindu is recommended. Sunnis can be found in the western part of Borneo, Sumatra, and the Malay Peninsula, while Hindus can be found in the eastern part of Borneo, Java and Bali. In order to convert to chosen religion, the player should conquer so many provinces following it, that they would make over half of the national development. Then sending a missionary at zero maintenance can provoke the rebels to activate, and accepting their demands would change the state religion. Alternatively, staying Animist until the Europeans arrive is a possibility as well, westernizing will fire an event converting Tidore to a Christian religion of their European neighbour.