Part one imo was simply the introduction and touching on the back story with the current situation. All the jutsu, characters, and events were all a tease for part 2 which is where i think kishi really wanted to focus. Part introduced the real threat to the series and delved into the truth of...
She may be "from the otherside" similiar to Father from fma. Possibly over the duration of wars a sacrifice was made or a ritual performed and the "exchange" took place forming her existence to save the world...but like father it backfired only to repeat a cycle of trial and error until now the...
I also believe Hashiramaʻs power with mokuton stem from the God Tree and also Madaraʻs sharingan from the same source albiet from the bloomed "eye" of the tree. Two powers of the same source the two of them were just the most in tune with their reincarnated halves