So i was looking at the tail section wiring of my '99 and i noticed a female end of a wiring plug hooked up with the factory wires. there is a cap on the open end of it. its right under my bed close to the back edge. i was wondering if anyone had any ides of what it could be. (i was thinking a plug to attach a trailer wiring harness to but idk). Thank you for any input you may have!

 

No idea with your description, maybe a picture would help

 

If it is 4 wires then yes, a trailer hook up.
There are also some pre-wired for canopy cargo light and 3rd brake light in canopy rear window

Wire colors for trailer lights here: How to wire up the lights & brakes for your vehicle & trailer