Majora's plan

Majora would have destroyed Termina with the moon,if not for the fact that Skull Kid didn't destroy or keep the Ocarina of time.Which let Link rescue the 4 giants in 3 short days.

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Bowser's Super Mario 64 plan

Bowser shouldn't have trusted that Rabbit with the key to the castle, which would've kept Mario out, andBowser would've suceeded.

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Ganondorf's plan in OoT

Had Ganondorf Killed Link before he reached the Temple of time,Ganondorf would've ruled for much longer,and since Link would be dead,there would be no descendants to challenge him.

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Smithy's plan

Smithy minionscould've destroyed the stars,and the power of wishes would've been gone forever.

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SMG ***Spoilers***

Kamek Had the chance to Kill Mario,but he didn't take it.Idiot!