Complex sentence: They do not achieve the second objective, as the primary systems of the craft are severely damaged, although in some episodes (including "The Flight Plan") Burton implies it is only a lack of fuel which prevents the ship lifting off.
Split into simpler sentences: They do not achieve the second objective since the primary systems of the craft are severely damaged. Although in some episodes (including "The Flight Plan"), Burton implies it is only a lack of fuel which prevents the ship lifting off.