Sognante had some interesting ideas about finding Cortana’s good fragments. From the two trailers we saw, it looks like Chief is going to try to trap Cortana in his “weapon containment device”, i.e. Cortana’s old helmet chip. My best guess: The E3 Discover Hope trailer is the START of the game, picking up in the aftermath of a huge battle on the Halo ring between UNSC, Created, and… Banished. This battle is likely to have stopped the firing of the ring, or it’s a battle for the Mantle. Banished have now been hinted at in their Halo Mythos story guide and in Halo Wars 2. Personally, it would be ridiculous to bring back the original Covenant or Storm Covenant again, as literally their entire militaries have disbanded. Original Covenant is now the Swords of Sanghelios, led by Arbiter, and Storm was wiped out in H5.
Anyway, this huge battle has left our beloved old characters scattered, making it unlikely we’ll see many of H5’s characters like Locke, Blue Team, etc. 343i is trying to go back to Halo’s roots, focusing back on Marines and not a surplus of super-soldier characters. I also think the plot will remain simple, not over-stuffed like Halo 5. 343i cited H3 and Reach as story inspiration, which were both simpler, but grittier, games. 343i also said Halo Infinite is a spiritual reboot that new players can easily hop into. For that reason, I think a lot of the complications introduced in H4 and H5 will be sidelined or dropped, including characters, overall arcs, and heck, maybe even the Guardians.
Personally, I think the story will pick up right from Discover Hope. Our first mission is Chief battling the Banished, who are sucking their ship up in the tractor beam. He’ll return to the Halo ring to retrieve Cortana. Her motivations may still be as galaxy dictator, or feeling immense guilt for the fallout of her actions. Either way, he’ll trap her in his weapon containment, purging her from the Domain, and the two will have to traverse across Banished forged warlands to try to reverse the damage the Created have caused. With both of their trailers, I honestly don’t see any situation where Cortana doesn’t have a redemption arc in this game. Maybe she’ll even lose total control of the Created to Warden Eternal.
As for the Flood’s return… eh, hard to say. Halo usually sticks to two enemies. There’s always a Covenant faction of some sort, i.e. Banished, and now the Created. But I wouldn’t be surprised if Prometheans were replaced or wiped out with Flood or something. I would love to see the Flood, but every time the parasite returns, it makes the Forerunner’s entire Halo galaxy purge even more pointless and wasteful.
It seems like, to me, 343i wasn’t expecting all the immense story criticism to Halo 5, which put all their “Reclaimer Saga” storylines in jeopardy. So, while this is the sixth Halo game, it’s not the Halo 6 that would’ve initially followed Halo 5 and continued the Reclaimer Saga’s themes and stories. It’s a reboot, and I think a lot of things will be retconned as it paves a new path forward.