I've got this mystery Connector near the alternator connector and the #2 fuel injector and can't find where it goes to. Any ideas?

Guess I should've said this is for a 2002 3.8L N/A Impala.

You just kind of found it. If everything is OK don't worry about it. They use the same harness for more options.

I tend to agree with carfixer007 ^^^^^^^

Does anything not work and/or is the check engine light on?

I'm more concerned with this:

I'm not sure about the spare cut wires but the one in your hand sure looks like the MAF Sensor connector.

The MAf sensor wires are three wires. That 2-wire female connector looks more like something going to the EVAP (gas tank purge) solenoid? Are there any CEL'* showing and if so, what are they from a capable scanner?

My guess is that it IS (or, namely, WAS) the plug for the #2 injector, and something happened that led to what is there now (which doesn't look like it came that way).

I guess the next question would be, where do those strange UN-sheilded wires from the alternator go to?