Assuming you are flying from USA to Athens to start your trip. Then ending your trip in Crete to go home.
Normally, folks get a roundtrip ticket to Athens. You should start your trip in Crete and end it in Athens, as getting back to Athens can have problems in Greece (strikes, weather). If you arrive in Athens on an overnight flight, you could book a separate afternoon flight to Crete. Touring Athens at the end of your trip gives you a cushion before your flight home.
Edited to add: Flights within Europe are cheap. I normally fly to or out of Greece from another country (where I have my roundtrip flights from the US), but I have the ability to visit friends before or after that flight, so I'm not worried about missing connecting flights on separate tickets. Otherwise, you may want to spend an overnight between those flights as a cushion, which won't work for you if you have limited vacation time.
I use www.skyscanner.com for searching intra-Europe flights.