Brotherhood of Steel ending
Brotherhood ending: Maxson attacks the Institute, destroying it and its synths. The Commonwealth is secured by the Brotherhood, at the cost of the Railroad and other factions.
Fallout 4
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Fallout 4's ending is decided by the faction you choose after reaching the Institute. There are four outcomes: the Brotherhood of Steel destroys the Institute, the Railroad frees the synths, the Minutemen destroy the Institute or you take over as its leader. Shaun's fate depends on the path: he can die in the assault, give you his place or be left behind.
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Brotherhood ending: Maxson attacks the Institute, destroying it and its synths. The Commonwealth is secured by the Brotherhood, at the cost of the Railroad and other factions.
Railroad ending: the Survivor sabotages the Institute from within, freeing the synths. The Institute collapses and the synths gain independence, though the Commonwealth remains unstable.
Minutemen ending: the Survivor leads the Minutemen to destroy the Institute with a bomb. The settlements are safe, and the Minutemen become the main power.
Institute ending: Shaun names the Survivor as his successor. The Survivor runs the Institute and may wipe out the other factions.
The story is about what you do for family. The Survivor spends the whole game looking for a child and finds a man, and the ending asks whether they will protect the Commonwealth, avenge their spouse or hold on to the last link with Shaun.
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Every sentence above is built from facts confirmed by at least two independent sources. Sources used: Wikipedia, Fallout Wiki.