The troubles in Northern Ireland related to politics, not religion as is often portrayed. When it is, they mention Catholics and Protestants. There is now a power-sharing agreement between representatives of the unionist/loyalist community, mostly Protestant, and the nationalist/republican community, mostly Catholic.
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Northern Ireland was another religious fight. This time it was between the Protestants and the Catholics.
Because not all of Ireland was free. 6 of the 32 counties were still under British rule, forming Northern Ireland.
Ireland is divided up into two countries; Northern Ireland and Republic of Ireland. The North is apart of the United Kingdom and therefore the fighting is about the Catholics/Nationalists wanting to be apart of the Republic of Ireland while Protestants/Unionists wanting to remain in the UK.
There has not been fighting between the Republic of Ireland and Northern Ireland. There was fighting between England (Britain or the United Kingdom) and the Irish when all of Ireland was part of the United Kingdom. The treaty that ended that fighting created the Republic of Ireland in the south and Northern Ireland (still part of the United Kingdom) in the north. After that, the IRA (Irish Republican Army) used violent means to try to push the British forces out of Northern Ireland and reunite the entire island. However, the Republic of Ireland did not participate in that activity and did not fight the British in Northern Ireland.
The same reason religious conflicts arise anywhere: because religious groups fight over their differences no matter where they are.