And that's where I find myself at now, digging through someone else's wiring, loads of fun. The two pictures attached are where I'm assuming something got hot and melted through, there's a newer crimp on the two wires.
My suggestion.
First, learn how the system is supposed to work.
Second, identify any factory options and all equipment alternations by previous owners.
Use the shop manual for your year and model to identify the circuit positions in the multi-connector.
Then you can figure out what was modified, and maybe why.
Knowing all the above you can come up with a repair plan that will be reliable.
The terminal on the alternator marked "Batt" feeds the main junction.
Current should never flow into it. It can happen when things go really wrong... Lets not go there right now unless there is evidence pointing that way.