I cannot catch the soldier in the Graveyard to get the captain's hat!! I have tried about 100 times!! When I play the Song of Storms nothing happens and I cannot get past Flat. I am stuck at this spot. Please help me.

Well here is what I did:

1st: You play that song to get him up and he will start running.
2nd: I just kept hammering him with arrows and then equipped the Bunny Hood.
3rd:Run up to him and pass him, then he will begin to fight you. ( I just heard the louder music and I knew he was gunna attack me )
4th: just beat his face in and he will take you to the start and he will make the fire surrounding the Chest disappear, than run over and receive the Captins Hat.

I doubt you will be back, but in future use the help thread

SPOILER!! (I think...)

Play the sonata of awakening
defeat the stalchilds, whislt shooting arrows at the captain to keep him still
slash away!!

remember the slashing

Yep! thats the most important bit of the process!! good luck!

I like to either use Goron Link and use the Goron pound, or use Link and use the spin attack while attacking the giant stachild with arrows.

That had to have been one of the more touching cutscenes in the game, I think.

It was really kind of sad.

I agree.
BTW, use Link's spin attack (not the charged up one, the one where you spin the control stick and hit B)and hit him with Ice Arrows. If you run out of Magic, just fire regular arrows fast enough so he doesn't get away. If you run out of arrows, turn into Zora Link and use your boomerang fins.