Link's Awakening is an interesting game. The ending is practically ruined from the get go as you are told that you must wake the Wind Fish as you are trapped on the island of his dream and you yourself are dreaming. Even the title tells how Link must awaken. So it makes me wonder.
Who is the real enemy here? When you go to get your OWN sword you are attacked by monsters and then the owl tells you to go to the dungeons and Maron (who is a representation of Zelda) tells you how to escape the island. Isn't she aware that if he wakes up she will cease to exist?
And whose dream is it at the end of the game the Wind Fish is flying, yet all the monsters in the dream are ones Link has fought including the nightmarish form of Ganon.
Here is the reality, the monsters attack you because they know that they are the parts that you want to forget. The people in the dream are all those that you want to remember and they will live on.
The Wind Fish has had a nightmare that won't end and since Link is a great hero who can overcome anything he uses his memories for the battlefield as his own would eventually kill him with them being so hopeless. The music represents lullabies to help ease the nightmares and in a last ditch effort it tries to silence Link for good.
In the end the real enemy is Link and the monsters just want to live that is why they are attacking. Link feels guilty which is why he must face a terrible enemy before getting his instrument. His guilt increases so does the strength of the monsters.
Ganon is his worst nightmare which is why the Fish's nightmare takes this form at one point. Link wants to see his friends and so do they which is why they keep helping him to wake up. When the nightmare is over the Wind Fish can rest easily and Link can reach home and avoid the monsters for good.