A "typical" Security system uses at least a green, blue, red, yellow, white, violet, black,orange, brown wires connected to the "main plug" wich if you unplug it from the"box", the sys. is unopperative 'cause the red wire feeds the sys. with (+)positive charge. The car should work ok, we can work with stereo, lights etc, later. There could be other small plugs with 2 or 3 wires attached. A "remote start" at least adds a bundled of four relays (1x1 inch little black box) to the sys. The cutted wire easily could be the atenna, if it is a remote sys., tipically is a black or green wire and it's free standig, no connection here. Fuses shuld be on the red and white wires of main plug.
Hope this help ID your "black box". If indeed it comes to be
a sec./sys. a reputable audio-alarm shop can easily remove it for you or maybe a friend with skills and knowledge.
Can You please tell more about: "from the manual, it was sopposed to be right there"?