So we know Cortana gained Guardians. I think she can use them to conquer and subdue previous Covenant species including Brutes, Drone, etc.
She may force Brutes to unite under her control. Obviously, campaigns wouldn’t be varied and diverse without Covenant.
Covenant would fear and worship Cortana as forerunner. The galaxy may be divided into two: ones who follow her and ones who disobey her.
I really hope 343i takes the opportunity to bring back missing species.
The missing species plus some new one’s we’ve never seen would be awesome.