Decompressing a string
Indentation. If you are using Eclipse, please select all your code and press Ctrl + I. Your entire for-loop should be indented one step further.
Use methods. One method for inputting a String, one method for making one iteration of the "decompression".
Did you forget about how to properly use indexOf suddenly? You use indexOf as a condition for your while loop, that makes sense. But then you're using a for-loop to determine the location of the ( and ) characters you are going to work with. This makes no sense to me.
Better variable names. Thanks to your comments on your question, I managed to figure out parts of what you are doing and write a review about that. However, Daniel still has a point that your code is not readable.
Close the scanner. Your scanner is a resource that needs to be closed, call sc.close(); as soon as you are done with the scanner (that is, after you have received all the required inputs from it)
Potential problems. What if I want to encrypt the string (thisWillMessWithYourCode2), how should that string be encrypted in order to be decrypted correctly? Or what would happen if I gave your program the input 42)invalid(data? I believe your code would have a hard time with that.