In the 2018 Short Treks episode, "Calypso," the self-aware computer of the starship Discovery — Zora — tells a castaway from the future the ship has been empty for almost 1,000 years. But why? In the 2019 Star Trek: Discovery Season 2 finale, we got a hint of the answer: The ship and crew jumped from the year 2257 to 3187 to prevent a malevolent A.I. called Control from destroying the universe. That's 930 years, which is pretty close to Zora saying she'd been alone for "nearly a thousand years." But when and how did the crew of the Discovery leave the ship empty? And how did Zora evolve exactly?
With Discovery Season 3 coming in 2020, figuring out the mystery of Zora and "Calypso" might be the storyline that unlocks everything.
Speculation for Discovery Season 3 ahead, also spoilers for Season 2 and Short Treks.
"I was ordered to maintain position."
That castaway, Craft, asks Zora to fly him home to his planet Alcor IV in the USS Discovery. She tells him she can't move the ship from its current location. Craft implies Zora's orders were issued by "a Captain who has been dead for "a thousand years." Craft doesn't know any more about why the Discovery is there than we do, but he knows it's from "the long ago." He also mentions that his enemy, the V’draysh, "cherish things from the long ago." In the Season 3 trailers for Discovery, when Michael Burnham meets a new character named Book, who mentions that Burnham must "Believe in ghosts" because of the "badge on her shirt."
In this future, roughly 3187, Starfleet, and probably the Federation don't really exist anymore. At least not in the way we've come to expect.
"Clearly, my records are out of date" — When Zora talks to Craft about Alcor IV, she mentions there wasn't a human settlement there, but then points out her records are out of date. This could be because Zora's records are still contemporaneous with 2257, or, it could mean something else entirely.
There's another wrinkle here. Back in 2018, the writer of "Calypso" and Picard showrunner Michael Chabon confirmed that the word "V’draysh" was a linguistic distortion of the word "Federation." This is sometimes called a "syncope," when letters and sounds are removed from the pronunciation of a word. (Trek has done this kind of thing before, most notably in 1979's The Motion Picture– the life form that calls itself V'ger took its name from the 20th-century deep-space probe Voyager-6.)
This implies that some aspect or faction of the Federation may morph into the "V’draysh" between the time of Picard and Discovery Season 3. This doesn't necessarily mean the "regular" Federation is gone in Discovery Season 3. In the trailers, we've seen Burnham meeting someone who is showing her a new version of the Federation flag, only this time, there are fewer stars on it; indicating that a lot has happened with the politics of the galaxy since the 23rd, 24th and even, 25th centuries.
So, are Zora's records really out of date about the year 3187? Or is she hiding something?
"I evolved" — Assuming the roughly 1,000-year time interval is relevant (and it feels like it has to be), then it seems obvious that the missing crew of the Discovery must have a connection to how Zora evolved to become totally sentient. In "Such Sweet Sorrow Part 2," the crew of the Enterprise briefly evacuates Discovery and tries to blow it up. Bizarrely, Discovery doesn't allow this to happen and raises its own shields even though nobody is on board. This seems to strongly suggest that the friendly A.I. who will become Zora was already developing back in 2257. By the time of "Calypso," Zora has a complete personality, and Chabon has implied Zora had several personalities, names, and genders before she met Craft. 1,000 years (or 930) is a long time, after all.
So how does all this fit into with what we already know about Discovery Season 3? At the end of "Such Sweet Sorrow Part 2," the crew takes the ship through a wormhole created by Michael Burnham's time crystal suit and follows her into the future. We don't see what happens next, but we do know from the trailers that Burnham will be separated from the crew for some undetermined period of time.
That probably has nothing to do with the entire crew evacuating the ship. Burnham was already on her own when they all traveled through time. That means the explanation as to why the crew left Discovery is still forthcoming.
"There's only one shuttle" — In "Calypso," Zora tells Craft there's only one shuttle left on the USS Discovery. Strangely, she also tells him the shuttle was brought onboard fairly recently: "We'd only just taken delivery. It didn't even have a name."
This could be a weird clue. In "Such Sweet Sorrow Part 2," several shuttles and fighters from both Discovery and Enterprise shield Burnham from the Section 31 fleet. By the time the battle is over, you really get the sense that all of the shuttles ended up back on Enterprise, if only because anybody going back to Discovery would also be taking a one-way ticket into the distant future. So why does Discovery only have one single shuttle in "Calypso"? And why does Zora say they took delivery of it so recently that it didn't have a name? Zora could be simply mentioning that the shuttle was actually from the Enterprise, but if that was the case, it doesn't seem like it would be brand new.
This suggests there's another explanation. Either Discovery got a new shuttle from someone in the far future, there's a lot more to Zora's story than we know. If Discovery Season 3 sticks to the mysterious twists of the first two seasons, it stands to reason that the seeds for those plotlines will either all lead toward the mysterious events of "Calypso." The biggest question underlying all of this is quite simple: Will Zora be a major character in Discovery Season 3?
Star Trek: Discovery Season 3 does not yet have a release date.