Infinite is a reboot.While it might pedal back in some areas there’s a thin line to tread, if we look at what we have in play we have Chief, Brohammer, Escharun, Cortana, and the Harbinger. each one possible making up their own faction. That’s 4 already if the flood are introduced that would be 5 in total, what worries me from the little bits we know of the story if the flood are also brought in it could potentially crowd the whole thing.
It's story has to act as an introduction for newcomers, a non-confusing welcome back for lost fans, and an interesting story diversion for those who have played Halo 4 and 5.
Obviously we know it's going to be about the Banished and zeta-halo.
But I don't see any reason why the flood can't take on part of that story. They are integral to the lore of the Haloes themselves - and as a reboot the Infinite story is sure to step back over such key points. They also serve as a (vital) refreshing mix up to the combat. And let's face it... if the Humans and Covenant (Banished) are fighting over the control of a Halo - the flood are going to get released (it's almost a horror trope of it's own).
There will be plenty of time to touch on Cortana - probably while discussing / dealing with the various human and Covenant AI's. They don't have to do a lot... just some backstory to get everyone up to speed... and then a visit from Cortana at some stage. She could just swoop in... help or hinder John... and leave with an ominous message... and hey presto, you are ready to move on with those narrative arcs in the next Campaign installments.
You would think (and hope) that they will keep it relatively simple.
For the newcomers at least.
Chief vs the Banished on a new Halo. It doesn't need to be much more complicated than that.
Clearly defined good guys vs clearly defined bad guys.
The Pilot replacing Cortana makes it easy to reheat and re-serve up a lot of the backstory (he can honestly ask the "who was that" type questions). And landing on a new ring, particularly the zeta-halo, makes it easy to retell the story of the rings... of which the flood is an integral component.
Overall I wouldn't be surprised if we essentially get an Episode VIII like retelling of Halo CE... just with the Banished instead on the Covenant per se. And the story notes will unfold more with the Chief answering the Pilot's questions (instead of Cortana / Chief).
Cortana will get 'introduced' early with the Chief having a bro-moment with the Pilot... and lots of little nods like the Chief feeling for his empty AI slot. Or maybe even with them finding an early version of Cortana. Late in the game Cortana will make an appearance to mix things up a bit... and do some evil forshadowing to stir up intrigue for the next game.