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In order to get access to the second floor of the Mog House you have to do all 3 of the Mog House short cut quests. I will paste the link below for the second floor main page. Basically you just have to take a certain flower to a Mithra child in Basty, Sandy and Windy located outside one exit of the Mog House. She will tell you the secret for getting access to exiting your Mog House to any area in that city.

The page below will have all the hyperlinks and explain how to get to the second floor. Skyfiredancer (talk) 12:05, October 6, 2015 (UTC)