Star Trek: Discovery has ruffled feathers with its aesthetic and plot lines, with assumed continuity errors causing assumed conflict with a lot of existing Trek series that take place after. The Star Trek: Short Treks episode "Calypso" appears to have addressed one of those issues, and it possibly clarified the USS Discovery's place in the franchise's canon. Specifically, we might know why the Discovery's advanced tech was never implemented on other Starfleet ships, and why Season 1's main crew isn't around later.
According to this far-flung Short Treks episode, something will likely happen in Star Trek: Discovery that results in the crew's disappearance, along with the ship itself apparently getting stuck in a holding pattern for 1,000 years until Aldis Hodge's character Craft wakes up inside it. With the ship having its specific position for that long, it seems the Discovery and its experimental technology were lost in space. This may explain why advancements such as the Spore Drive didn't find their way to other vessels in the franchise.
"Calypso" was set 1,000 years after the events of Star Trek: Discovery, and followed the unfamiliar Craft after his escape pod was rescued by the Discovery. Craft learns the ship is completely unmanned, but that he's not exactly alone. The Discovery's artificial intelligence had evolved into a sentient program that named itself Zora. Zora explained she'd been holding the Discovery's position for the past millennium under the instruction of a long-missing captain.
So, the good news for Star Trek fans is that we, at least for now, have an explanation for why the Discovery's developing tech and its crew aren't directly referenced in "future" shows. The bad news is it sounds as though something crazy is going to happen to Michael Burnham, Tilly, and the rest of the crew that results in their fates being unknown in that distant future. What happened to the crew, and why did they completely abandon everything like that?
We're not completely sure yet, of course, but if Spore Drives aren't commonplace in lots of known Federation ships in the future, that probably means folks like Paul Stamets aren't around to share their knowledge of the mycelial network. Perhaps the crew gets transported back to the parallel universe, and can't find a way back this time around.
It's also possible the crew isn't lost and presumed dead, but that they just haven't returned yet from wherever they are. Star Trek: Discovery's introduction of time-travel in Season 1 could easily lead to some pretty wild plot lines going forward. I mean, this mini-episode set up the notion that Starfleet ships might all be capable of evolving into sentient beings if given enough time. So Michael intentionally or unintentionally taking a 1,000-year jaunt into the future isn't the most far-fetched idea.
There has to be a reason the ship was instructed to maintain that position, and we're guessing it's for another reason other than the obvious "captain leaves, and no one returns" song and dance that kicks off other space-faring dramas. It seems like someone is destined to pop up there other than Craft. As for who it could be, or why it happened, Season 2 could offer up some big clues. Let's just hope Zora finds someone else to talk to after "Calypso" rolled its credits.