Warning: SPOILERS for Star Trek: Discovery Season 3, Episode 9 - "Terra Firma, Part 1"
What happened to Ambassador Spock (Leonard Nimoy) is no longer a mystery in Star Trek: Discovery season 3's 32nd century. The influential Vulcan time traveled and crossed over into a parallel universe in J.J. Abrams' Star Trek 2009, and this is where the elderly Spock spent the remaining few years of his life before he died in the Kelvin timeline in 2263 - a fact that the United Federation of Planets wasn't aware of for centuries but is now tacitly knowledged in the year 3189.
Spock was famed as the First Officer of Captain James T. Kirk's (William Shatner) Starship Enterprise in the 23rd century but after he ended his legendary Starfleet career, Spock followed in his father Sarek's (Mark Lenard) footsteps and became a Vulcan Ambassador. Spock's personal crusade was the reunification of the Vulcan and Romulan peoples and he spent years trying to bridge the divide between the cousin races, which brought Spock into contact with Captain Jean-Luc Picard (Patrick Stewart). When the Romulan sun went supernova, Spock attempted to save the planet but he was blown backward in time and into the Kelvin universe created by another time traveler, the Romulan villain Nero (Eric Bana). Ambassador Spock ended up helping the younger, alternate reality versions of Captain Kirk (Chris Pine) and Spock (Zachary Quinto) defeat Nero and, later, Khan Noonien Singh (Benedict Cumberbatch). Sadly, Spock never returned to the Prime timeline and the Federation assumed he was a casualty of the Romulan supernova. His proper timeline had no idea that the Vulcan hero died in another time and in another universe.
Star Trek: Discovery season 3, episode 9, "Terra Firma, Part 1" revealed that the Prime timeline's Federation became aware of the Kelvin timeline when a time soldier named Lt. Commander Yor crossed over during the Temporal Wars. Yor, who wore a Star Trek: The Next Generation-era uniform, was a Starfleet Officer who jumped forward from the Kelvin universe in 2379, which was 166 years after Ambassador Spock's death. Unfortunately, Yor died a gruesome death because of the deleterious effect the combination of time traveling and breaching from a parallel dimension has on the body, but before Yor expired, he must have told the Federation everything he knew about his point of origin, including the fate of Ambassador Spock, who is also the only known person who jumped from the Prime to the Kelvin universes.
Unfortunately, the revelation that time travel and crossing parallel universes destroy a person's molecules adds a grim dimension to Ambassador Spock's death. It was assumed that the Vulcan icon died from old age since he was 161 at the time of his passing. Yet 161 is still relatively young for Vulcans, who have been known to live beyond 200 years (Sarek died at 203). Star Trek: Discovery's update about the frightening hazards of simultaneous time/dimension travel indicates that Spock must have also suffered an agonizing death in the Kelvin timeline.
After all, Ambassador Spock lived in the alternate reality for 5 years; by contrast, on Star Trek: Discovery, Emperor Philippa Georgiou (Michelle Yeoh), who also time traveled after crossing over from the Mirror Universe, is rapidly deteriorating after just a few weeks in the 32nd century. However, perhaps the fact Georgiou time-traveled forward 930 years compared to Spock's 129-year journey backward contributed to the Emperor's quick decline, and Spock's Vulcan physiology probably allowed him to endure the pain and hang onto life longer than a human could have.
On a happier note, Spock's legacy in the Prime universe was crystalized because the unification he dreamed of came to pass when Vulcan welcomed the Romulans home after the supernova destroyed their planet. Although it took centuries, the Romulans and Vulcans have managed an uneasy but peaceful co-existence and, as a symbol of their rejoined destinies, they gave the planet Vulcan a new name: Ni'Var. It's comforting to know that the Prime universe's Federation did eventually learn the truth about Spock traveling to the Kelvin timeline so that the Starfleet legend's fate is no longer a mystery in Star Trek: Discovery's 32nd century.