Bugsee can authenticate with Github through either Basic Authentication (login/password) or OAuth. If OAuth is used, Bugsee wizard will redirect you to Github which will prompt you to grant Bugsee permissions:
Basic Authentication & 2-factor authentication
If 2FA is being used, Basic Authentication can not be used, OAuth is the the only option. Once the user authenticates Bugsee to Github the integration will continue working as long as the token is valid.
Read more at Github: https://developer.github.com/changes/2013-09-03-two-factor-authentication/