According to one embodiment, a heavy oil may be processed by a method that may include upgrading at least a portion of the heavy oil to form an upgraded oil, where the upgrading comprises contacting the heavy oil with a hydrodemetalization catalyst, a transition catalyst, a hydrodenitrogenation catalyst, and a hydrocracking catalyst to remove at least a portion of metals, nitrogen, or aromatics content from the heavy oil and form the upgraded oil. The method may further include passing at least a portion of the upgraded oil to a separation device that separates the upgraded oil into one or more transportation fuels; and where the final boiling point of the upgraded oil is less than or equal to 540° C.