Sounds to me like a couple of circuit breakers, or relays, installed by either the PO, or by his mechanic or a stereo installer for some aftermarket accessory. Try testing the wires for juice...with a volt meter...not by touching them to each other.
Molded connectors can be had at ANY parts or electronics store giving it a "stock" appearance. Like said above, a picture says a thousand words. You might need to show us what you're describing.
I have an aftermarket circuit breaker and 4 extra relays for lights and other accessories. It does NOT look stock...but some guys, or their mechanics are very skilled at adding electronics and other modifications. Not me, but some guys. Mine works fine, not pretty,but functional.
1990 XJ Laredo - White & Chrome
1988 MJ Pioneer - Metallic Green and Black