[cmonref]

I take it that you replaced the externally-regulated alternator with an internally-regulated alternator? And in that process removed the three pin female connector from the bottom of the regulator and removed the now-unneeded regulator. And now you are now wondering what to do the the female connector just hanging around the left side of your engine compartment?

The wires in the connector are still "hot" so you must prevent them from grounding against something. An appropriate dieelectric covering, taped or tie-wrapped in place, would do that job.