Complex sentence: It is his orders concerning this journey that appear to be confused: it appears it was initially planned merely to hasten the return of the polar party (in order to give them a chance of catching the ship), and not as a relief mission.
Split into simpler sentences: It is his orders concerning this journey that appear to be confused. It appears it was initially planned merely to hasten the return of the polar party (in order to give them a chance of catching the ship), and not as a relief mission.