Clocking in at twenty episodes, the first season of Magic Knight Rayearth gave us a solid little fantasy series with the three girls saving the world of Cephiro, discovering what a deep love is and learning a lot about themselves. When it ended and they were sent back to Japan, you knew it was just a matter of time before something drags them back again. At twenty-nine episodes, the second season of Magic Knight Rayearth takes us back to a very different Cephiro and adds in a lot more characters and settings and invariably drags it out a bit more than it should. Or a lot more in some cases.
While life has seemed a little bland and empty since returning, the trio all get together at Tokyo Tower again to catch up on things. As would happen, the light flashes and they're sucked back to Cephiro. Cephiro this time around is not the world of bright greens and blues and a myriad of creatures and settings. It's a devastated world, one where it's all dark and blackened as catastrophe has fallen. When Emeraude and Zagato bonded together, her role as the Pillar ended. The lack of one in the world to guide peoples hearts and to be guided by the people has caused Cephiro to fall to ruin. All that's left is a crystal spire castle where Clef has brought all the people to so they can try and figure out what to do. It's not Noah's Ark though as the only creature there appears to be Mokona.
Cephiro is still hoping for a new Pillar of pure heart to appear that can take on the role, but right now the darkness is a despair caused by the hearts of its people. What makes it worse is that there are three other countries, which are displayed and viewed as very separate worlds, that are attempting to take over Cephiro itself. With the appeal of the Pillar being able to do whatever they want, not realizing what the downsides are, they're intent on capturing it and using it to secure an advantage. The three groups are all very distinct cultures that play off of standard stereotypes so there aren't too many surprises here, though again we see a few hints as to what CLAMP does in some of their future works.
Source Here: http://www.mania.com/magic-knight-rayearth-season-2-remastered-set_article_121485.html