Thats a mess. Thats not factory as you guessed. I have no clue what that is brand or model wise. What does the front of the remote look like, the back side is shaped like the factory fobs.
If you want to remove that black box, you'll need to get the model and or brand off it and try to find an installation manual to backtrack through. Some systems have you cut wires and splice the module in between the cut, some just require a splice into the wire without cutting it apart. Its difficult to remove security systems without causing problems without taking the time to study the system before messing with it, or having an install manual.
This one looks pretty basic, it certainly can be removed without causing the vehicle to stop functioning.
