It helps them rise!! Duuuuuh!!
P.S. It's just like with bread!!!
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Lol nice way of putting it. I still think my way is better though! >:D woooooooh, im a space ship taking away random cookies if their flat!
The flour creates gluten, which helps the cookies have structure. In some cases, it even adds to the flavor. Basically it holds it all together.
Its just there so the cookies can rise! Its not like a space ship will take the cookies away if their flat!