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    Pre-Release Theories 

Pike actually DID see himself die in the vision
What the audience was shown was somewhat of an abridged version because we already know what happens, but In-Universe there were some differences-namely, Pike saw the exact moment his life ended.

However, as we know, it won't turn out exactly as he saw-because he confided in Spock about it, which will allow for a change through some application of Exact Words and Loophole Abuse-Pike can't change his own future, but Spock can; which will lead to the events shown in "The Menagerie" (and retroactively explain why it was worth it to Spock to commit mutiny to save Pike.)

Pike will somehow avert You Can't Fight Fate as a result of his vision
This aversion could take one of many forms. It's highly unlikely he'll commit suicide to do so. He could become a Death Seeker in order to seek a Heroic Sacrifice to make sure he actually dies. Or he could do something to prevent his incapacitation in 2266; or an attempt to prevent it could lead to him actually dying.

Or, assuming he actually did see himself die—and he could've meant when he said he saw his actual death that he regarded his incapacitation as equivalent to being dead—he could do something that results in his ultimate incapacitation as originally seen in "The Menagerie".

Something happens to Dr. M'Benga's career during the course of the series
In TOS, we know that Dr. McCoy is the Chief Medical Officer of the Enterprise by the mid-2260s, and Dr. M'Benga shows up as one of his subordinate medical officers on occasion. Yet, during the earlier period chronicled by SNW, Dr. M'Benga is still the CMO of the Enterprise. Either M'Benga voluntarily steps down from the CMO position at some point, or Dr. Piper and then McCoy are assigned or promoted over his head for some reason.
  • Dr. Piper might have what the military refers to as 'time in grade' over M'Benga. What this means is that they could be of equal rank, but Dr. Piper might have been promoted to said rank a year before M'Benga, making him the superior officer. Another theory could be that when Pike does get injured, M'Benga (obviously being a close friend) might take a leave of absence to help care for him, and in the meantime, Piper, then later, McCoy, come aboard as the CMO of the Enterprise. M'Benga might come back, but now he's the lower-ranking doctor.
    • The latter may well be the case. In A Quality of Mercy we see that, in the Alternate Timeline where Pike remains Captain of the Enterprise in 2266, M'Benga is still the CMO and there's no sign of McCoy. This does seem to imply that M'Benga's career on the Enterprise as CMO is tied to Pike's own career/fate.
  • Perhaps M'Benga finds a way to partially cure his daughter, and steps down as full-time CMO to care for her. Or she goes to live on Earth, and M'Benga transfers to a planetside post, occasionally doing brief tours on the Enterprise.

    Season 1 Theories 

Spock and Chapel have an affair
In TOS, they were both engaged to other people, but Chapel was obviously attracted to Spock (more ambiguous if he felt any attraction towards her or not). In SNW, they both become equally attracted to each other, have a fling, and break it off out of guilt.
  • Played with in The Serene Squall, when Spock and Chapel pretend to be having an affair to convince T'Pring to end her relationship with Spock, thus allowing her to refuse Captain Angel's demands in a way that preserves her reputation.

La'an Noonien-Singh is an Augment
She's not just a distant descendant of Khan, but an Augment from the same Eugenics War era. Like Khan's group, they set out on a sublight colony ship... which instead of being found by the Enterprise like the Botany Bay was, it was found by Gorn. Cue all the horrific things that happened to the crew, and La'an being the sole survivor. Like Julian Bashir a century later, she's holding back to not draw attention and doesn't give details on just what is entailed by "colony ship" when talking about her past. Dr. M'Benga may be aware of it and is keeping it a secret as well.
  • She is indeed descended from Noonien-Singh, and thereby partly "augmented". Which lead to tension when she discovered that her best friend and mentor, Una Chin-Riley was genetically modified.
  • Her status is pretty much confirmed 100 percent human as a) she is a known descendent of Noonien-Singh and b) any form of augmentation automatically barrs her from Federation service and is an automatic court-martial as seen with Una Chin-Riley. So she is not augmented in any fashion or degree.

The timeline in Episode 1 is deliberately erroneous.
Pike shows footage of the 2021 Capitol riot and implies it predates the Eugenics Wars (dated to the 1990s). This is not supposed to be an actual retcon from the writers, but an implication that the Future Imperfect trope is in play. Either the Eugenics Wars are initially thought to have happened later than they actually did (a mistake which gets corrected by the TOS timeframe), or the Capitol Riot is not actually a predecessor to the Second American Civil War, and the footage Pike used was mistakenly labeled as such.
  • Given that Pike's goal was to make a point and not necessarily to provide a history lesson, he may have been conflating the various events together.
  • It may also be telling that the names of one of the cadets changed from Muliq Al Alcazar in episode 2, to Maat Al-Salah in episode 10.

Spock and Uhura will develop a mentor/protégé relationship.
They have a lot of scenes together in Episode 2, with Spock often offering Uhura advice and encouragement, and they even perform a duet of sorts on the comet. Their Commonality Connection is that they're both "too honest" and they're knowledgeable about the mathematics of music. In the Kelvin timeline, he was her Advanced Phonology instructor, so the showrunners seem to have been inspired by that and are portraying Spock as Uhura's mentor in the prime timeline. It's worth noting that a deleted scene from TOS shows that he taught her how to play the Vulcan lute, and he mentions the complex mathematics of this instrument.

Hemmer will die saving the ship at some point, inspiring Spock to do the same in TWOK
In "Memento Mori", Hemmer comments that the Aenar believe that one can't die until they have fulfilled their purpose. Uhura asks him what his purpose is, to which he replies: "To fix what is broken." It's hard not to see this as foreshadowing — at some point in the future, he'll die in a Heroic Sacrifice to save the ship and her crew, Scotty will be brought in as his replacement, and the incident will be what inspires Spock to pull a similar stunt in the climax of Star Trek II: The Wrath of Khan.
  • Scotty didn't join the Enterprise until 2265. Also, Pike was known for going through engineers (they either die or transfer off the ship. Proof of this is how in Discovery, the engineer was a man named Louvier and then, three months later in SNW, Hemmer comes aboard, and now Hemmer is dead).
  • Confirmed: He dies in "All Those Who Wander"note , and Spock acknowledges the logic of his decision.

M'Hanit was created by the Proto-Humanoids from "The Chase"
In the Star Trek universe, all humanoid life in the galaxy is canonically descended from an ancient race that seeded the primordial oceans of millions of worlds with its own genetic material. Presumably, M'hanit from "Children of the Comet" and the other comets like it were created to continually "nudge" evolution on those planets in a direction that promotes the survival of lifeforms with a humanoid body plan.

Samuel Kirk was the jester that Rauth (Pike) would have summoned if M'Benga hadn't declined.
This would fit if it were made an exaggeration of his don't-touch-that moment in "Children of the Comet".

The dog from "The Elysian Kingdom" is real.
This can be proven both by how it took part in the dramatic staring contest, and how M'Benga doesn't make any technobabble when scanning it.

The Travelers/Supervisors were involved in enforcing Spock's death in all the timelines in which Pike avoided his fate
It seems a little convenient that apparently nothing Pike does can save the cadets, himself, and Spock all in one timeline. Perhaps the Travelers somehow manipulated events to force Spock's death in all the "wrong" timelines so that Pike had to go with the correct one. As a corollary to this that might make them seem a bit less heartless, maybe they also Tricked Out Time and recruited the two cadets who were supposed to die into the organization while faking their deaths, because the Bad Future wasn't their fault, and they had no idea what would happen.

The Gorn infants from Star Trek: Strange New Worlds S1E09 "All Those Who Wander" are the Gorn's attempt at creating augments.
Even ignoring Bones's comment from Star Trek Into Darkness about Gorn breeding habits, these baby Gorn are faster and more vicious than the adults seen in their debut in TOS, and are somehow not only fertile within hours of hatching, but are able to inseminate another humanoid simply by projectile vomiting at them. If it wasn't for the 'last man standing' nature of their hatching, this could potentially give them a reproductive rate on a par with tribbles.

    Season 2 Theories 

Kirk comes aboard as second or first officer
It's already been announced that Paul Wesley enters the role of James T. Kirk in the second season of SNW, yet the producers keep clarifying that Captain Pike will remain in charge during the series. It seems likely that Kirk will show up as a mid-level to senior officer, probably a lieutenant commander or commander from the Farragut or another starship, and work his way up to succeeding Pike as The Captain. It's also entirely possible that Number One might earn her own command at some point in the interim, creating a vacancy as the executive officer of Enterprise that allows Kirk to be assigned to the ship.
  • Something like what could have happened when Picard was taken by the Borg, they bought on Shelby as a Borg specialist, kept the rest of the crew in their specialized positions, made her the XO and bumped up Riker to Captain.

Alternately, Kirk comes aboard as the new Chief of Security
La'an has been Put on a Bus already, leaving a vacancy as both Chief of Security and Second Officer. What we know of Kirk's career background would fit that dual position very neatly.

Scotty comes aboard as an engineer.
He joins the crew as a lower ranking officer, but works his way up the ranks and becomes Chief Engineer by the time of TOS.
  • Season 1's finale did feature a brief voice-over from a certain engineer in an alternate timeline...
    • Given that Hemmer is dead as of the end of Season 1, the Enterprise does need a new Chief Engineer...
    • Scotty doesn't come to the Enterprise until 2265.

The events of the Season 1 finale altered the timeline.
Pike's round-trip to the alternate 2266 in "A Quality of Mercy" may have altered the Prime Timeline slightly. Pike now knows (or at least believes he knows) that Kirk will be his successor as Captain of the Enterprise, and he's shown to be researching him even when he returns to the present. It's possible that, knowing this, he seeks out Kirk and they end up meeting years before they originally would have (which according to Kirk in "The Menagerie" was when he first took over the Enterprise from Pike). He also learned about Una's fate in the alternate 2266, and that's also something that he'll no doubt be working to change. These changes, significant in themselves, will no doubt lead to other changes, resulting in a Close-Enough Timeline that broadly matches the backstory established by the original series, while serving as a handwave for retcons.
  • Not necessarily. For all we know, the Pike from TOS had gone through the experience of seeing his time crystal on Boreth (which happens after the events of "The Cage") which would fit in nicely with the events of "The Menagerie", where Pike is reluctant to go to Talos IV as he believes his life is over. Moreover, Pike knows better than to mess around with the timeline and will probably keep an eye on Kirk and will ensure he succeeds him as captain of the Enterprise, which is probably how he got the command all along.

    General/Miscellaneous Theories 
The Gorn will be the "Borg" of this series
La'an's backstory and the prominence of the Gorn warship in the series trailer both seem to hint at this.
There's no fate but what we make for ourselves.
There will be a scene of Christopher Pikes' near feature. With years of training, Christopher Pike will beat the 'No Win Scenario,' and save all the cadets and himself. Almost. Only to find there is/was another cadet to save. Their remains found decades later. Laughing, while about to succumb to wounds, Pike is rescued by an unknown Starfleet Admiral.

Dusting off Pike the officer mutters, 'Jean-Luc would be disappointed.' Before Pike can ask his million questions, the Admiral has Pike look after the cadets. Q has a rare expression of sadness. 'Fate can be postponed. But it can't be cheated.' Q snaps his fingers only to find nothing happens. 'I'm dying??' Q snaps his fingers again.
The No Win Scenario
Captain Pike creates 'The No Win Scenario' training exercise.
  • The timeline doesn't support it. Kirk took the test when he was a cadet (probably shortly before the events of Star Trek: Discovery), and at this point in the timeline he's already a commissioned officer.
Uhura‘s hairstyle represents a visual timeline.
When Uhura first enters the show, she has a very short hair, almost completely shaved down. In the next episode, her hair is slightly grown out.Celia Rose Gooding is deliberately using this to show how close in time Uhura is to the TOS timeframe. Celia Rose Gooding’s hair will be progressively longer throughout the show until it’s close enough to the style Nichelle Nichols wore on the original Star Trek.
  • Potentially Jossed in the Season 1 finale A Quality of Mercy where we see Uhura in 2266 during the events of the TOS episode Balance of Terror and Celia Rose Gooding has the same short hair she does wile playing 2259!Uhura. Then again, it is an Alternate Timeline, so maybe in the Prime Timeline she will start gradually growing her hair to resemble Nichelle Nichols'.
Brent Spiner as the 23rd Century ancestor of Dr. Noonien Soong will appear as a mentor to Roger Korby
We've seen a Dr. Soong in every Century so far EXCEPT the 23rd. Brent Spiner willing, gotta keep up the tradition. And given Arik's comments in ENT, the 23rd Century Dr. Soong would be pursuing robotics instead of genetics. "What Are Little Girls Made Of?" established that Korby was a former flame of Chapel and Akiva Goldsman has hinted he will show up at some point. So perhaps Korby starts out as an assistant to Dr. Soong before he strikes out on his own with less successful results.
Dr. Boyce will appear in an episode
Dr. Boyce will visit the Enterprise, portrayed as having retired sometime between the events of “The Cage” and the beginning of this show. He will cure an alien plague or have a similar major medical accomplishment.