I guess you have FortiAuthenticator (FAC hereinafter) set with RADIUS Service, so defining which FortiGates (or simply whoever 3rd party talking RADIUS) is able to authenticate via this FAC.
That RADIUS Client is probably set to authenticate against some 'realm' which is probably your AD.
So user auth requests (RADIUS Access-Request) will come and will be processed against AD (via LDAP) by FAC.
So pay attention to 'REALM' (Authentication > Realms) and if it's LDAP type (your AD), then it has switch 'Chained token authentication with remote RADIUS server'!!
You have to have set both (LDAP for your AD, AND! RADIUS for your 2FA) in Authentication > Remote Auth. Servers .. and that RADIUS will then be useful in above mentioned chaining from LDAP realm to RADIUS 2FA.
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