Your right, you can use the pen in scratch to have your projects draw! Some people even make projects that generate different patterns!
Here is an example of a simple pen script:
[blocks]
<when green flag clicked>
<clear>
<pen down>
<set pen color to( blue
<move( 5 )steps>
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The pen tool can be used for many things. When you press pen down a line follows where your sprite goes but the stamp tool can be just as useful as the pen tool if you know how to use it look at my tutorial to learn a little bit about the stamp tool
http://scratch.mit.edu/projects/RapKat/1677545
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