In the quest, "Mything Link" Both Cyrus and Merle Ambrose indicate that Mandrake has not been seen in Wizard City for many years. You are then told that Mooshu has the only remaining Mandrakes. However, since the introduction of Crafting, Red Mandrakes can now be found in many Wizard City zones.
Seperately,
After finishing the pre-Celestia quests and talking with most of the NPCs in the beginning of Celestia, no one really knows who is behind the destruction. In Thurston's message he refers to that person as the Umbra Queen and only gets out the letters "Mor." However, Llewella Corey in Celestia Base Camp tells you that Morganthe laid seige to Celestia for the Astral magic. How does she know more than Halston and Thurston so early on? Her revealation shouldn't come until the Crusteacean Empire portion.