You will be asked to enter the password that was used to encrypt the Aegis vault. The same password will be used for resulting KDBX database.
Limitations
This tool does not support changing existing databases, atk creates a separate clean database for your TOTP codes. You should not store TOTP secrets in the same database as your passwords anyway, since this removes all the benifits of having a second factor in the first place.
This tool also does not accept unencrypted Aegis JSON files (yet, at least) as input