How to Open: You have to water the mysterious plant in front of the clock
tower and climb the resulting beanstalk.

(if this is what you're talking about)
-Fin-
Step 1: Head STRAIGHT south, not taking the stairs. If you did this correctly, you should exit out of a small gap near a spawn portal
Step 2: Now take the stairs leading south-west from here
Step 3: Move to the south-east, taking the series of stairs
Step 4: Ignore the stairs leading south to the Tower of Rest, and keep moving east
Step 5: Move north until you pass through the gate
Step 6: Move a small distance east into the Flank

http://www.gamefaqs.com/wii/946789-rune-factory-frontier/faqs/56323