The game I am currently working on will consist of a top down and side scroller hybrid for exploration. Top down to explore the overworld map and side scroller when going into towns, buildings, random battle encounters, etc. The problem is I am trying to conduct more research on how to implement the two into one. Are there any tutorials that can get me in the right direction for either unity or GMS2? any advice would help.

Perhaps you can draw some inspiration from how Keen (1, 2, 3, 4, 5, 6) and Vinyl: Goddess from Mars did it?