OK, here's my half-baked idea. It won't happen, and I don't think I'd want to it, but...
So we were told that this season would explain why Spock never mentioned Burnham, but narrative rules suggest that two people who begin in a state of estrangement will reconcile by the end of the story, so something's gotta give. Either Burnham gets erased from Spock's mind, or something happens to permanently separate them. Are there other options?
So let's try this: the
Discovery crew finds out that not only is someone trying to wipe out life in the galaxy, but that they're from the far future, 1000+ years, and they're trying to change the course of history to prevent the Federation from becoming what it will be. And the Red Angel seems to be trying to stop this. So
Discovery will need to hop across 1,000+ years to solve the mystery and thwart the enemy. They're literally in a fight for the future.
How will they get there? They can't use the spore drive--we saw how temporally unreliable that was--but they come up with a way to move just a skeleton crew (Mudd's time crystal?). How will they move the ship? There are two paths to the future: they're taking the short road, but the ship will need to take the long way round.
So they give
Discovery some simple automated maintenance and defensive subroutines and hop through time. They rendezvous with the ship to discover that she's sapient now, and calls herself Zora. And they realize that the thing that called them to the future was in fact
Discovery herself, who has been sitting, monitoring, charting history, becoming alive. Some kind of downfallen Preserver-equivalent enemy has set out not to save but to end civilization, and they're reaching across history to do it by changing little things a la
A Sound of Thunder. And it's bad news: the future, as it stands, is a place where things fall apart for the Federation, now the backwards-looking, self-obsessed V'Draysh. But Zora knows what needs to happen: send one of them back, using advanced future tech, to intervene in a few critical events, the proverbial butterfly effect. And someone, maybe Burnham, is sent through time at Zora's behest, fixing the timeline and thwarting the enemy in the guise of the Red Angel.
In some kind of suitably epic showdown, everything the anti-Preservers have been up to is prevented, and a future where the Federation survives is maintained. But for whatever reason they can't all make it home, and Burnham and most of our cast (save Pike and Spock) are stranded 1000+ years in the future, with a sentient ship and a brave new world.
But there's one last butterfly effect act that needs to be carried out to pave the way for the world that will be. The season ends with Christopher Pike returning to New Eden to welcome Jacob and his people into the Federation.
OK, time to go to bed.

(I don't really think this will happen. And I'd rather Disco stay in its century. But I'd love for Calypso to be relevant to what happens!)