1. First create a secret and associate it with a user
2. Next create a QR code and let the user scan it:
   
   ...or display the secret to the user for manual entry: OFZR 5NXO MZCD HKRU B5MM O44X D2P7 EGU3
3. Next, have the user verify the code; at this time the code displayed by a 2FA-app would be: 138670 (but that changes periodically)
4. When the code checks out, 2FA can be / is enabled; store (encrypted?) secret with user and have the user verify a code each time a new session is started.
5. When aforementioned code (138670) was entered, the result would be: OK

Note: Make sure your server-time is NTP-synced! Depending on the $discrepancy allowed your time cannot drift too much from the users' time!