Here is the summary of the 3 volumes of the Manga which make up for Part 2 of the series (episodes 21-49 in the TV series). Do please note that this is an edited version of the summary written by Camille of Smashed Ice, proper credit should be given to her. Any personal comments included are hers also.
The second series starts with all three girls in their respective homes, all looking really sad and droopy. They meet at Tokyo Tower again, and all of them are really downcast because of what happened with the princess and
Zagato. But all of a sudden, they fall through the floor again, just like last time.
They end up in Cefiro again, to find the world in turmoil again because there's no "Pillar". Three other countries, or rather, three other groups of people, are trying to get into Cefiro by building pathways, the leaders hoping to become the next "Pillar" of Cefiro.
There's Eagle Vision from the country of Autozam, which is one of those technological countries where people convert their willpower into other stuff in order to have all kinds of high-tech machinery and stuff like that. Eagle wants to become Cefiro's "pillar" because the atmosphere in Autozam is really messed up. Then there's the two princesses of Chizeta; they're twins who have these two genie things to protect them. They want to get Cefiro because their own country's land area is way too small. And last of all is this little girl-spoiled brat princess Asuka, from the country of Faren, who wants Cefiro because.....well, she just WANTS it.
Anyways, all three of these countries are fighting to get into Cefiro to become the "Pillar". The thing is, however, to become the Pillar you have to have a heart/will that's stronger than anyone else's. The three knights decide to help fight on Cefiro's side to keep those three countries out. They also meet some interesting new characters like Lantis, who's Zagato's brother and who wants to destroy the Legend of Magic knights (doesn't mean he wants to kill the current 3 knights) so that nothing like what happened to his bro and the princess will ever happen again. He's also Cefiro's only magical swordsman. But anyway, after you're chosen as one with a strong enough heart/will, then you have to pass a test to become "Pillar".
It turns out that Mokona, the little rabbit-type creature (he's SO cute) is the creator of the world (talk about CLAMP's sense of humor), and Eagle and...Hikaru are the only ones with strong enough wills to qualify for "pillar". They are taken back to Tokyo to battle it out, but Hikaru talks to Eagle (while fighting), and stresses the feelings of all the heartbroken people left behind when one becomes "Pillar" of Cefiro...you're unable to love anyone. Eagle admits that he wants to become Cefiro's "Pillar" because he has a disease, and will die soon, so he has nothing to loose.
However, Hikaru's speech really moves him and also proves that she has the stronger will, so SHE becomes the next Pillar of Cefiro. But when the Pillar is chosen, the other person who lost the fight disappears forever. Hikaru doesn't want Eagle to disappear, so she drags him back to Cefiro with her...it's really touching (from my point of view anyway) because she gets all cut up and stuff trying to take him with her, and when he tries to make her stop, she reminds him that he's got to keep on living for all the people that love him.
Well...as you can probably guess, they both made it back (with help from Umi and Fuu, who also get kind of messed up trying to meet Hikaru on the path and take her back). As the new Pillar, Hikaru ops to abolish the Pillar System to leave Cefiro in the hands of its people who truely loves it. The world is restored, and the girls are able to come and go to and from Cefiro as they please.
