I am doing a 12 day tour in Bulgaria and want to extend the trip by 3 days in Greece. We love history, not adverse to short hikes, museums, or beaches. Would like to get off beaten track and would be willing to hire a guide. We would fly from Sofia to Athens. Any suggestions would be appreciated as I was thinking we could spend 3 days in Athens using it as a base to go elsewhere. Thank you in advance.

I will assume you mean you have 3 NIGHTS which then means you have less than 3 days. It’s almost nothing but if you were going to base in Athens, and assuming your flight arrives at a time where you can be checked into your hotel by noon, I’d recommend:

1. Day 1: Acropolis and Parthenon. Possibly New Archeological Museum
2. Day trip to Delphi
3. Other Athens sights. Plaka. Icon Museum, etc.

Athens is not my favorite city, save for the Acropolis and Parthenon. With such a small amount of time, is there some reason you feel compelled to fly all the way to Athens after 12 nights in Bulgaria?

Should you wish a guided tour while in Athens, recommend Athens Walks, a small company started by Kostas, a former Evzone (Presidential Guard). You have a choice of several different private or group tours, all led by licensed guides. One of the favourites is the gourmet food tour. Not everyone likes a guided tour, but these get rave reviews.
https://www.athens-walks.com/

Iif you travel 2 weeks through Bulgaria, you may visit places close to the Greek border, like Melnik. If this is the case, check whether it makes sense to backtrack to Sofia in order to fly to Athens.