Warning: SPOILERS for Star Trek: Lower Decks Season 3, Episode 5 - "Reflections"A hilarious shoutout to J.J. Abrams' Star Trek movies by Ensigns D'Vana Tendi (Noël Wells) and Samanthan Rutherford (Eugene Cordero) on Star Trek: Lower Decks could secretly mean Starfleet in the 24th century is aware of the Kelvin Timeline. In Star Trek: Lower Decks season 3, episode 5, "Reflections," Rutherford's implant malfunction allows his previous personality to become dominant, and it drops more hints about the insidious reasons Sam received an implant in the first place. But there is the further possibility that Rutherford's implant contains secrets about the Kelvin Timeline that he doesn't fully understand.
The Kelvin Timeline was created when the Romulan starship Narada commanded by Nero (Eric Bana) time traveled from 2387 to 2233 and destroyed the USS Kelvin, which was led by Lt. Commander George Kirk (Chris Hemsworth), the father of James T. Kirk (Chris Pine). This incident initiated an alternate reality where numerous events happened differently from the original Prime Timeline of Star Trek. In the Kelvin Timeline, Jim Kirk became Captain of the USS Enterprise much sooner, Spock's (Zachary Quinto) homeworld of Vulcan was destroyed by Nero, and the Enterprise battled Khan Noonien Singh (Benedict Cumberbatch) years earlier and under very different circumstances than in the Prime Timeline. In Star Trek Beyond, the Starship Enterprise was destroyed and replaced by the new USS Enterprise-A. Starfleet's technology also evolved at a faster pace and interactions with races like the Klingons fared differently in the Kelvin Timeline. However, it was not clear whether the Prime and Kelvin Timelines were aware the other existed in the 23rd or 24th centuries.
Star Trek: Lower Decks season 3, episode 5 primarily deals with Rutherford learning the truth about his implant and his forgotten past, but it also kicks off with an amazing joke about J.J. Abrams' Star Trek movies. When Rutherford confesses to Tendi that he's been losing sleep because of nightmares, she asks, “Is it the one where you’re in a new timeline with Kirk and Spock, and they have cinematic chemistry?” On the surface, this could just be read as a knowing wink by the animated Star Trek comedy, and Lower Decks has jokingly referenced the Abrams Star Trek in the past, such as in Lower Decks season 1, episode 9, "Crisis Point." But what if there's even more behind Tendi's quip? After all, Rutherford is routinely bombarded with information from his implant that he chalks up to "malfunctions." Yet, what if Rutherford just doesn't realize that his implant's details about "alternate timeline Kirk and Spock" are actually real? Could this mean Starfleet in the 24th century knows about the Kelvin Timeline, and Rutherford is unaware what he thinks are nightmares is actually facts encoded into his implant?
Star Trek's Prime Timeline Crossed Over With Kelvin On Discovery
Star Trek: Discovery season 3 revealed that the 32nd century United Federation of Planets has long been aware of the Kelvin Timeline. Temporal Wars were waged centuries before that threatened the Multiverse, and even the Guardian of Forever (Paul Guilfoyle) hid in the Beta Quadrant rather than be used as a weapon in the Temporal Wars. Dr. Kovich (David Cronenberg) revealed to Dr. Hugh Culber (Wilson Cruz) that a time soldier named Lt. Commander Yor from the 24th century of the Kelvin Timeline crossed over into the Prime Timeline, although he soon died from the physical stresses of jumping time and realities. However, it's possible that Starfleet's awareness of the alternate Kelvin Timeline happened even sooner.
The Federation is aware of the Mirror Universe in Star Trek: Lower Decks' era, so it stands to reason they may have also become aware of the Kelvin Timeline. By Star Trek: Discovery's 32nd century, there's an awareness of the Multiverse, and the truth of parallel timelines could very likely have proliferated by the 24th century, even if it's kept under wraps by Starfleet for obvious reasons. Star Trek: Lower Decks' joke about an alternate reality Kirk and Spock may indeed have deeper layers and possibly even ramifications further down the line.
Star Trek: Lower Decks Season 3 streams Thursdays on Paramount+.