Hikaru, Fuu, and Umi are once again transported to Cephiro. But, with the Pillar gone, they don't know how they could have been transported back. As they meet up with old friends, they find that Cephiro is now crumbling because they do not have a pillar. They also find that gates from other worlds have opened, and the leaders want the Pillar to themselves for their own selfish reasons. Hikaru, Umi, and Fuu must now set out to save Cephiro form dying.

Magic Knight Rayearth 2 was published in English by Tokyopop from June 2000 to June 2003 as volumes four through six of Magic Knight Rayearth. Tokyopop rereleased the series as a collector's edition box set. Dark Horse Comics later took over the license and published the series in omnibus volumes on April 11, 2012. The series has been published by Kodansha USA since July 15, 2025. It was also published in Brazilian Portuguese by Editora JBC in six volumes from January 2002 to June 2002.