Hey @otterman23,
I hope the answers below will help.
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Q: Forest Zone, couldn't find any bosses in the Tower of Time?
A: You have to defeat the bosses in Zone 3 to unlock the bosses in the TOT
Q: How do I get to the next area?
A: Each Town has a Hall of Transference, defeat Medusa in the Castle of each zone to progress to the next area.
Q: What are the plants used for on the farm?
A: The plants are used in Alchemy to make potions; this will become available in update 1.7
Q: Do I have to be Jack?
A: No. Speak to Alex, the NPC at the top of the map by the stairs in the Church Basement.
If you notice any bugs / glitches, please let me know so I can fix them.
Thanks for playing!