WARNING: The following contains spoilers for Star Trek: Lower Decks Season 2, Episode 10, "First First Contact," streaming now on Paramount+.
Star Trek: Lower Decks pulled out all the stops for its Season 2 finale, with "First First Contact" showing just how inventively effective the Cerritos truly is before completely shocking the crew to their core with a major twist to end on a massive cliffhanger. And while the crew manages to make it through this harrowing ordeal in one piece, unlike the Season 1 finale concluding with Lieutenant Shaxs' heroic sacrifice -- before his unelaborated resurrection later in Season 2 -- it's clear that life will never be the same for the Cerritos as it loses its commanding officer, Captain Carol Freeman.
In Season 2's penultimate episode, "wej Duj," the Cerritos discovered a plot that involved a rogue Klingon commander supplying the deadly Pakleds with advanced weaponry to destabilize the Federation. The Cerritos was able to fend off the Pakleds, with the timely assistance of a nearby Vulcan starship, and the Klingons brought themselves presumably in line over a matter of honor, with Freeman sending a full report about her discovery to Starfleet Command immediately thereafter. And this report may have just shaken up something Starfleet was trying to keep a secret, as special investigators arrive on the Cerritos in the finale to arrest Freeman over allegations that she falsified the report while orchestrating a brazen attack on the Pakled home world.
After averting a crisis on what was initially a routine first contact mission, the Cerritos is boarded by Starfleet personnel, with Freeman expecting to be commended and offered a promotion for her exemplary leadership. Instead, Freeman is placed in restraints with the revelation that she has been implicated on a devastating incident on the Pakleds planet, with images showing the entire planet ravaged by what appears to be a massive explosion. The investigators allege that Freeman's prior report was meant to be a misdirect while she launched the unsanctioned attack on the Pakleds after the civilization had been menacing Starfleet ever since Season 1.
Though Freeman is confident that the truth will come out and clear her name, there is an implication that Freeman's report ruffled feathers somewhere in Starfleet Command over a matter that they wanted to cover up. The interplanetary exploratory and peacekeeping force certainly has possessed a dark side before and the Klingons may not be the only major presence in the galaxy arming the Pakleds while looking for a patsy to divert attention away from themselves. And in Freeman, the captain of one of Starfleet's most unassuming starships, they may have just found their perfect mark while continuing their illicit business elsewhere.
With Freeman's arrest, it's likely that Lower Decks Season 3 will begin with the Cerritos captained by a new commanding officer while Starfleet Command will probably be paying a lot more attention to the Cerritos' crew. Apart from watching her mother get arrested, this will also put the pressure directly on Beckett Mariner moving forward, with her usual freewheeling ways now restricted by whomever takes over the Cerritos with a more by-the-book policy. The Cerritos may have saved the day at the end of Season 2 but it paid dearly for doing the right thing this time, with the crew now targeted by someone further up the command chain.
Season 2 of Star Trek: Lower Decks is streaming now on Paramount+.