Warning: SPOILERS for Star Trek: Lower Decks season 2 finale, "First First ".
A shocking development in Captain William Riker (Jonathan Frakes) saved the Cerritos at the end of Lower Decks season 1 - Freeman is surprised by Starfleet Security and arrested for allegedly blowing up the homeworld of the Pakleds.
The Pakleds were a problem for the Cerritos throughout Star Trek: Lower Decks season 2. Building towards the Star Trek: Lower Decks season 2 finale, episode 6, "The Spy Humongous," saw a blundering Pakled spy infiltrate the Cerritos while Captain Freeman was trying to negotiate peace on Pakled Planet. Star Trek: Lower Decks season 2, episode 9, "wej Duj (Three Ships)," introduced the Lower Deckers of alien starships, especially the Klingon Ma'ah (Jon Curry), who stopped his Captain from colluding with the Pakleds against the United Federation of Planets. These elements built up to Star Trek: Lower Decks' season 2 finale, "First First ," where Freeman was taken into custody immediately after she led the Cerritos' first instance of making First with an alien race.
Star Trek: Lower Decks' season 2's outstanding finale upends the comfortable paradigm aboard the USS Cerritos once again. Freeman's arrest for treason is just as precarious for her rebellious daughter, Ensign Beckett Mariner (Tawny Newsome), as it is for the Captain and leaves both of their futures in doubt. With this latest upheaval aboard the Cerritos, here's where Star Trek: Lower Decks season 2's ending leaves the Cerritos' key crew going into season 3.
Captain Freeman Arrested: Was She Framed (All The Clues)
Starfleet Security arrested Captain Freeman at the end of Star Trek: Lower Decks' season 2 finale immediately after she achieved a career-high by leading the inaugural First by the Cerritos. Freeman is accused of conspiring with Klingon extremists to plant a bomb that destroyed Pakled Planet. Freeman was humiliated by being escorted off of her own starship in irons in front of her crew. Given what fans know about Captain Freeman, it's hard to believe that Starfleet Security is right and Freeman worked with Klingons to blow up a planet. The likely scenario is that Carol is being framed, but by who?
The only time Captain Freeman actually set foot on Pakled Planet was in Star Trek: Lower Decks season 2, episode 6, "The Spy Humongous." As she tried to broker peace between the United Federation of Planets and the Pakleds, Freeman and the resurrected Lt. Shaxs (Fred Tatasciore) were repeatedly frustrated by the idiotic Pakleds. They were essentially held prisoner on the planet while Commander Jack Ransom (Jerry O'Connell) hunted the Pakled spy aboard the Cerritos. However, at this point, the Klingon Captain Togg (Robin Atkin Downes) was likely already secretly working with the Pakleds to attack the Federation. It's possible the Klingons could have been also planning to betray the Pakleds and frame the Federation for destroying the homeworld of their "allies."
And yet, Ma'ah killed Togg and took over as Captain of the Klingon Bird-of-Prey Che'ta to stop the Pakled and Klingon alliance from destroying the Cerritos in "wej Duj (Three Ships)." Since Togg is already dead, this points to someone else working behind the scenes, who was possibly pulling the strings and knows the full story behind the Klingons' conspiracy with the Pakleds' strings. This would mean Captain Freeman is just a patsy caught up in a sinister, far-reaching plot. Regardless, Captain Freeman has been disgraced and has lost the confidence of Starfleet. She will likely stand trial while Mariner and her friends seek the truth to exonerate the Captain in Star Trek: Lower Decks season 3.
The Secret Behind Rutherford's Bionic Implant
Star Trek: Lower Decks' season 2 finale dropped further clues about the truth behind Ensign Sam Rutherford's (Eugene Cordero) bionic implant. Rutherford had the operation to install his tech before the series began but his implant has malfunctioned multiple times throughout Star Trek: Lower Decks. In "First First ," Rutherford suddenly saw a memory of mysterious surgeons operating on him and discussing how Sam would believe receiving the implant was "elective." Rutherford's eyepiece and why he has it in the first place could have an insidious purpose.
Rutherford is actually wearing his second implant after the original was destroyed in Star Trek: Lower Decks' season 1 finale. The process of losing his first bionic tech and getting a new one caused him to lose his memories of his best friend, Ensign D'Vana Tendi (Noël Wells), which caused Sam a lot of distress. Star Trek: Lower Decks season 3 could finally reveal the truth behind Rutherford's implant, and the fact that Tendi was transferred out of the sickbay and into training to become a Science Officer like Spock (Leonard Nimoy) may help Rutherford get to the real reason why he's wearing a bionic implant in the first place.
Boimler Kept Saving The Day In Season 2 (While Mariner Disappoints)
To save the USS Archimedes, which was damaged by a debris field and about to crash into the Luperian homeworld, Captain Freeman ordered all of the hull plates to disengage from the Cerritos. But it was Brad Boimler who heroically dove into Cetacean Ops and nearly drowned unlocking the last hull plate for the gambit to work so that the Cerritos could save the Archimedes. It was the ultimate heroic act by Boimler, who spent Star Trek: Lower Decks season 2 rising to the occasion and saving the day. Boimler also outwitted the Pakleds when he was still serving on Captain Riker's USS Titan and Bradward later defeated an evil computer named Agimus (Jeffrey Combs) who tried to pit him and Mariner against each other.
Star Trek: Lower Decks season 2 was a remarkable turnaround for Boimler, who was strictly by-the-book but insecure and inexperienced in season 1. In contrast, Mariner had a challenging season 2 where she worked more closely than ever with her mother, Captain Freeman. This curbed Mariner's ability to go rogue and also exposed some of her limitations and issues with command. Mariner even blanked when Freeman asked her to come up with a risky scheme to save the Archimedes. Mariner is now even more aware that her career wearing a Starfleet uniform has depended on her mother's protection, and what it means for Beckett now that Captain Freeman is under arrest remains to be seen.
Will The Cerritos Get A New Captain In Lower Decks Season 3?
With Carol Freeman under arrest, the Cerritos will likely get a new Captain when Star Trek: Lower Decks season 3 begins. The California-class starship will also need to undergo repairs since it was completely stripped off its hull platings. Commanding a California-class starship isn't a sought-after position in Starfleet and Captain Freeman herself was about to be transferred to a new and better ship before she was taken into custody. This would seem to exclude possible top names like Captain Riker or even Captain Sonya Gomez (Lycia Naff) as the Cerritos' new Captain so there could be an entirely new character coming aboard to command the Cerritos at the start of Star Trek: Lower Decks season 3. It could even lead to a nightmare "Captain Jellico (Ronny Cox) situation" for Mariner and the crew.
How Star Trek: Lower Decks' Season 2 Ending Connects To TNG
Star Trek: Lower Decks' season 2 finale heroically went all out in homaging Star Trek: The Next Generation's season-ending shockers, right down to using TNG's famous blue "To be continued..." font and Chris Westlake's score mimicking the ominous music heard when TNG ended a season with a cliffhanger. For Star Trek: Lower Decks, Captain Freeman's arrest is as tumultuous as Captain Jean-Luc Picard (Patrick Stewart) being assimilated by the Borg in "The Best of Both Worlds" or Worf (Michael Dorn) leaving the USS Enterprise-D to fight in the Klingon civil war in "Redemption."
Further TNG connections include Star Trek: Lower Decks finally showing Cetacean Ops, which was mentioned in TNG but never seen on the show itself. In addition, Sonya Gomez was merely an Ensign when she was introduced on TNG but Star Trek: Lower Decks revealed Gomez rose to become Captain of the USS Archimedes and a close friend of Captain Freeman's (who also mentored a young Will Riker before Riker took on Beckett Mariner as his protege). Star Trek: Lower Decks takes pride in continuing the style and feel of Star Trek: The Next Generation, albeit in a faster-paced, comedy format, and season 3 will continue the Cerritos' wacky adventures even as it resolves the cliffhanger of what will happen to Captain Freeman.
Star Trek: Lower Decks is available to stream on Paramount+.