Maybe in an alternate universe, the writers decided:
En route to penal colony, Michael gets rescued from a Klingon attack by Discovery. Saru becomes acting captain after the captain dies during the mission. Saru gets the exact same arc.
Michael gets stuck on DISCO because war. A bunch of people got killed rescuing her so now they need people in engineering, so she has something to do, and she feels double-guilty.
There is no Lorca, meaning we don't have to go to MU at all. We get to spend that time on getting to know the Klingons as real people/culture instead of props standing in circles in the pilot. (Don't get me wrong, Lorca was great but since he was thrown in the garbage why not just delete him altogether?) Through L'Rell's eyes we see the toll of war and feel them coming to the brink of internal collapse. Maybe the Orion Syndicate has been using the Federation/Klingon conflict as a way to take over Klingon Empire, so Clint Howard still gets his green cameo.
Stamets just deteriorates throughout the season, and the mycelial network weakens due to our misunderstanding and misuse of the it. (If this was supposed to be DISCO's environmental allegory, blaming it all on the evil MU was a serious cop out.) Now we can't make more spore ships and magically beat the Klingons with magic. (Though if you still want to make the MU sojourn for the purpose of showing Burnham a glimpse of !Voq then this could have been handled in a single-episode spore drive malfunction.)
Saru's Kelpian fear of predators and general distaste for mutiny predispose him to agree with Starfleet's plan to nuke Kronos, a plan that gets hatched immediately after the midseason break, because the cloak breaking schemes fail in the time-honored "Mr. Worf, fire" fashion. We spend the whole second half working on the bomb. We get to explore Saru's inner demons and see his struggle with fear vs. Starfleet ideals. Maybe we even have time to for EVERYONE on DISCO to weigh in (Lol, jk).
Michael and crew have to convince Saru there's another way. They hatch a plan with L'Rell, who has spent the season not in the brig, but on Kronos where she has witnessed firsthand that the current path is destroying her people too. It would have been actually interesting to see a fundamentalist revise her views over the course of the season based on her actual interactions with humans. Rather than magically changing because she's been in a cage for months.
All zero-sum Michael/Lorca stuff and Michael/!Georgiou stuff is now replaced with Michael/Saru stuff, which was genuinely interesting in the first few eps and had great potential before being reset. (Think of the friendship we got from Bashir/O'Brien S1 conflict.) It still gets to be a redemption arc for her finally at the end of the season earning Saru's trust and forgiveness. She still loses Tyler, but she has gained a friend or two--not unlike the end of Casablanca (though I realize Casablanca is not a TOS episode).
She waits til the end of the last episode to give the telescope to Saru, at which point it would have been genuinely touching and a visual symbol of the ship getting back to its mission of "discovery".
This route would have been more coherent, told the same story, and requires zero twists (though Tyler/Voq could remain unchanged).