Complex sentence: In this story, Crowe battles not only with the Guild but with his former SIGMA partner and potential love interest, Cassandra Sanchez, as well, who is acting under the orders of the Guild.
Split into simpler sentences: In this story, Crowe battles not only with the Guild but also his former SIGMA partner and potential love interest, Cassandra Sanchez. Sanchez is acting under the orders of the Guild.