Majora's Mask takes place in a parallel version of Hyrule, hence why many of the characters are the same. If Termina was destroyed, it would not affect Hyrule.
As per the Temple of Time, Link seals Ganondorf in the Sacred Realm. Ganondorf swears vengeance (Skip to 1:10), and Link is returned to his own time. Although it isn't shown, the thought is that Link will emerge from the Temple of Time in seven years to defeat Ganondorf exactly how the player did. The ending would be much more clear if it showed Link being transported outside of the sealed sword chamber.
There are two Ocarina of Time Links at the same time - one of them is sealed in the Temple, the other is off looking for his friend Navi. Adult Link comes out of the Temple, defeats Ganondorf, and is sworn vengeance upon, then Link is sent back to the past. The Link that did all of this already is off adventuring outside of Hyrule.
Ganondorf's seal is broken, he attacks Hyrule, and according to Wind Waker, the Hero of Time never shows up.