Complex sentence: In the developing of the story Misato discovers that Kaji, besides of his work for Nerv, he secretly is also working for the Intelligence Department of Japan, and threatens to kill him if he does not desist from his sabotage plans.
Split into simpler sentences: In the developing of the story Misato discovers that Kaji, besides of working for Nerv, secretly he is also working for the Intelligence Department of Japan. Misato threatens to kill him if he does not desist from his sabotage plans.