Complex sentence: When Joe listens to the tape, he discovers that not only the mole's name but also the pronouns referring to them have been removed; he deduces from the removal of the pronouns that Sarah is the mole and that Alan had confessed to cover for her.
Split into simpler sentences: When Joe listens to the tape, he discovers that not only the mole's name but also the pronouns referring to them have been removed. He deduces that Sarah is the mole and that Alan had confessed to cover for her.