I am looking for the fuse for the plug in the left side box that you plug a topper into. Looked thru the manual and can’t find it. That wire is usually live all the time so you don’t have to turn the key on to light up the box area.

This is the connection location in the back

 

To my knowledge, that is not stock. Meaning it's an add on, aftermarket harness. You'll probably just have to trace it back to find the fuse, power connection.

 

The flat connector is a 4-pin flat trailer connector. Not sure the point of somebody mounting it there, but whatever. It appears they then tapped into it with the do-it-yourself crimp connectors for the red and black wires.

I assume you are using the wire for something and realize it is dead?
Look under the bumper where a hitch would be....the factor trailer wiring should be in that general area- considering there is a trailer plug in your picture I feel it safe to assume they could have tapped into the factory trailer wiring.
I'm out of guesses now...