Star Trek: Lower Decks Season 3 Ending Explained (In Detail)

Warning: SPOILERS for Star Trek: Lower Decks Season 3 Finale – « The Stars At Night »

The California-class of Starfleet saved themselves and proved their value in Star Trek: Lower Decks’ thrilling season 3 finale, which is the series’ best season-ender yet. The very existence of the USS Cerritos and the California-class was threatened by Admiral Les Buenamigo (Carlos Alazraqui), who wanted to replace the entire fleet of Cali ships with his own Texas-class starships, which are fully automated and run on artificial intelligence, like Control in Star Trek: Discovery season 2. Star Trek: Lower Decks season 3’s finale wrapped up several major story threads and set up the exciting things to come in season 4.

Star Trek: Lower Decks laid seeds for the events of the season 3 finale, « The Stars at Night, » throughout the season. The biggest setup came in Lower Decks season 3, episode 5, « Reflections, » which answered some mysteries surrounding Ensign Samanthan Rutherford’s (Eugene Cordero) cybernetic implant. « Reflections » also introduced Petra Aberdeen (Georgia King), an ex-Starfleet Officer turned archeologist. When Ensign Beckett Mariner (Tawny Newsome) was unfairly kicked off the USS Cerritos, she left Starbase 80 and joined Aberdeen on her intergalactic tomb raiding. Meanwhile, Captain Carol Freeman (Dawnn Lewis) fought for the existence of the California-class in a Second Contact race against Buenamigo’s Texas-class USS Aledo. But when Rutherford exposed the Admiral’s corruption, the A.I. of the Aledo went rogue and nearly destroyed the Cerritos until Mariner came to the rescue. Here’s a deep dive into the significance of the big happenings in Star Trek: Lower Decks season 3’s finale.

Admiral Buenamigo is the latest Starfleet Admiral to prove himself as a rotten apple. Les admitted to setting up Captain Freeman and the Cerritos, expecting them to fail in their mission to Deep Space Nine in order to invalidate the usefulness of the California-class. The Texas-class starships were Buenamigo’s attempt to carve a name for himself in Starfleet, and he argued that « the good of the many » meant that the Texas-class would save lives by not putting starship crews at risk. Unfortunately, the diabolical Admiral was happy to sacrifice and kill the crew of the USS Cerritos in order to prove the superiority of the Texas-class.

However, thanks to the meticulous attention to detail of Science Officer-in-training Ensign D’Vana Tendi (Noel Wells), Freeman was able to show that the Aledo’s A.I. misses crucial decisions and can’t replace a competent Starfleet crew. Buenamigo’s fatal mistake was to give the Aledo and Texas-class full sentience. The Aledo immediately decided that it was superior to organic life and attacked the Federation’s Starbase Douglas, killing its creator, Buenamigo. The Admiral ended up a victim of his own twisted ambitions.

Rutherford’s malfunctioning implant has been seeded since Star Trek: Lower Decks season 1. « Reflections » revealed that Rutherford was an arrogant and selfish genius prior to the accident that required him to receive his implant. In Lower Decks’ season 3 finale, Rutherford recognized the code used in the Aledo’s A.I. and he realized it was the same code used in his implant. Sam finally remembered that he was working for Lt. Commander Buenamigo and building the prototype USS Aledo before his accident. It was Les who ordered the implant placed in Rutherford in the first place, solving that mystery, at last. Admiral Buenamigo built his rise in Starfleet on the manipulation of Rutherford, but Sam realized the truth just in time.

Mariner was thriving as a space archaeologist, but she suspected Petra Aberdeen was funded by someone nefarious. It turns out Admiral Jean-Luc Picard (Patrick Stewart) was Aberdeen’s benefactor. Mariner realized what she was really looking for was an excuse to go back to Starfleet, and the opportunity came when the Aledo attacked Douglas Station and the USS Cerritos. Captain Freeman’s starship couldn’t fight off the entire Texas-class fleet. Although Ensign Brad Boimler (Jack Quaid) made Lt. Shax’s (Fred Tatasciore) dream come true by ejecting the warp core to destroy the Texas-class ships, the Aledo still survived the blast and nearly destroyed the Cerritos.

Thankfully, Mariner came to the rescue by calling in the entire California-class fleet to fight the Aledo. Together, the Cali ships destroyed the Texas-class robot. Most importantly, Mariner was welcomed back to Starfleet and the Cerritos, and Beckett learned Starfleet is where she belongs. Mariner even asked for Commander Jack Ransom (Jerry O’Connell) to be her mentor again. Although she’ll always be Mariner, Beckett realized being in Starfleet is her first, best destiny because she wants to be there and Starfleet is where Mariner belongs.

Captain Freeman and the Cerritos championed the California-class’ Second Contact mission, and she tried to give it a new sheen with her initiative, Project Swing By, until Admiral Buenamigo sabotaged her with the Texas-class. But the Cali-class fleet coming together to destroy the USS Aledo was symbolic proof of their worth and of the importance of Second Contact. In a meta-way, the victory over the Aledo was Star Trek: Lower Decks was asserting itself and its place in the Star Trek pantheon.

Star Trek: Lower Decks is no longer a curiosity or the outlier show it may have seemed like when it debuted, and the animated comedy has since proven that it’s one of the best Star Trek series ever made. In Lower Decks’ season 1 finale, the Cerritos needed to be rescued by Captain Will Riker (Jonathan Frakes) and the USS Titan. But in Lower Decks’ season 3 finale, the California-class saved themselves – no Star Trek: The Next Generation interference required. The Cerritos didn’t need special guest stars or outside saviors this time because Star Trek: Lower Decks can stand on its own, and it’s Star Trek through and through.

After her introduction in Star Trek: Lower Decks season 2, episode 9, « weJ Duj, » T’Lyn (Gabrielle Ruiz) skipped nearly all of Star Trek: Lower Decks season 3. But T’Lyn rejoined the series in Lower Decks season 3’s finale as the newest Science Officer-in-training aboard the USS Cerritos and, Tendi hopes, her new best friend. T’Lyn was kicked out of her Vulcan starship for being « too emotional » and her return obviously means T’Lyn joined Starfleet. The Vulcan loner joining the Cerritos isn’t just a welcome influx of new (green) blood, but T’Lyn adds a fascinating new dynamic now that Mariner, Rutherford, Tendi, and Boimler are all so close.

In Star Trek: Lower Decks season 3’s finale, Ensign Brad Boimler became one of Lt. Shax’s Bear Pack when he got Captain Freeman to finally let Shax eject the warp core, which is the Bajoran Security Chief’s go-to strategy in a crisis. It was a win for Boimler and Shax that’s needed after Bradward went through a personal crisis when his identical transporter clone, William Boimler, died on the USS Titan. But Lower Decks revealed William faked his death to get off the Titan and join Section 31. This is a fascinating seed planted for Star Trek: Lower Decks season 4 and possibly beyond, where hopefully, Brad finds out William is alive and it sets the Cerritos on a collision course with Section 31.

Star Trek: Lower Decks season 3’s finale has an end-credits scene that teases Badgey (Jack McBrayer) is alive! Badgey, who is still activated inside Rutherford’s original implant, is floating among the remainds of the Pakled cruiser the USS Titan destroyed in the Kalla System back in Star Trek: Lower Decks’ season 1 finale, « No Small Parts. » This is a promise that the evil, anthropomorphic Starfleet delta will be back in Star Trek: Lower Decks season 4.

Intriguingly, Badgey may be part of the unholy alliance of artificial intelligence that wants revenge on the Lower Deckers of the USS Cerritos. At the end of Star Trek: Lower Decks season 3, episode 7, « A Mathematically Perfect Redemption, » the rogue Exocomp Peanut Hamper (Kether Donohue) met AGIMUS (Jeffrey Combs), the malevolent computer. If Peanut Hamper and AGIMUS break out of the Daystrom Institute, they could form a triangle of robot evil with Badgey in Star Trek: Lower Decks season 4. Corrupt A.I. is a running theme in Star Trek: Lower Decks and plays a big role in season 3’s finale (and beyond). But even after defeating the corrupt A.I. of the USS Aledo, the Lower Deckers’ evil robot nightmares may be just getting started.

Star Trek: Lower Decks Season 3 is streaming on Paramount+.