From another website:
Majora's Mask is about Link coping with the death of Navi.
Each major area in the game represents one of the 5 stages of grief:
Clocktown=Denial
No one wants to admit that the moon will crush them, they just want to have their carnival
Woodfall=Anger
The Deku are furious at the monkey for "kidnapping" their princess. They completely ignore the fact that he has nothing to do with their swamp being poisoned.
Snowhead=Bargaining
If only the Goron's legendary hero would return, everything would be alright again.
Great Bay=Depression
With the lead singer's voice gone, the rest of the Zora mope about, seeing no point in anything.
Ikana=Acceptance
Filled with the dead, Link must bring peace and calm the lingering spirits there.
Some text from the Happy Mask Salesman:
"Whenever there is a meeting, a
parting is sure to follow.
However, that parting need not
last forever...
Whether a parting be forever or
merely for a short time...
That is up to you."
What was Link's mission at the beginning of the game? To find an old friend, right? What does Tatl say to Link after all is said and done, yet there is no Navi in sight?
"Well, both of us have gotten what
we were after..."