For the second entry in the Phantasy Star franchise we jump ahead 1000 years, where a technological revolution has swept over the Algo system thanks to the supercomputer Mother Brain. However, things are not all well as monsters once again begin to appear and no clues to their origin present themselves. So it falls to Rolf, the last surviving descendant of Alis from the first game, to set out and discover exactly what's going on.
This is the point where the series takes on a much darker edge, trading in many of its fantastic elements for cyberpunk and its relatively simple story for one much more gritty in tone. This is also where the series moved away from 3D perspective dungeons to entirely 2D maps, making them much more of a challenge to navigate.