use robin's helicopter to shoot a rope at the scarecrows plane then onece done emedietley switch to batman and shoot a bat bomb at scarecrow.
do the whole thing 3 times and you will have completed the level.
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Scarecrow will be unlocked and available in free play after you complete the third mission in the third villain episode: The Joker's Masterpiece. Alternately, you can enter the cheat code, see related questions below.
EDIT: Wait...this question wasn't for Arkham Asylum, was it? Oops. My fault for not reading the question and category right...but I hope this helps if you DO play Arkham Asylum!
Well...bad news, you face Scarecrow multiple times. Good news, however, is that it really isn't a boss "fight," per se.
When you face Scarecrow, don't let him see you. EVER. Just move around the platforms (counterclockwise works best), and detonate any walls that block you. Use the bat signal once you're reached your destination.
Best of luck with winning!
Wait until the hearts are red, then get out of the pumpkin, after use the batman boomerang.