Question

We’re performing a scene from my favorite book (the second in the trilogy).

Answer 1

I think the answer is A to your question 

Answer 2

The answer is D:

 The sentence "the second in the trilogy"  is a nonrestrictive element. That means that the purpose of its inclusion is to provide an additional information, which is not essencial for the meaning of where the perfoming scene came from.  Using a comma would normally come before this sentence, but the parentheses are used to modify it.