Season TWO
1 "Strange Energies"
The USS Cerritos is completing second contact with the planet Apergos when Ensign Beckett Mariner, the daughter of Captain Carol Freeman, discovers an ancient defense system while power-washing the buildings. It attacks Mariner, discharging a beam of energy that instead hits First Officer Jack Ransom and gives him god-like abilities. Ensign D'Vana Tendi becomes concerned that her friend Ensign Sam Rutherford's personality has drastically changed since he lost his memory and got a new eye cyborg implant. She attempts to fix them with her medical equipment, but scares him off. Tendi decides to implement more extreme measures, but soon realizes how she is treating her friend and makes up with Rutherford. Ransom goes mad with his new power and sends his giant, floating head into space to attack the Cerritos. On the ground, Mariner kicks his headless body in the crotch which diminishes his powers and eventually returns him to normal. On the USS Titan, Ensign Brad Boimler struggles while serving under William Riker.
2 "Kayshon, His Eyes Open"
After a prominent member of the Collector's guild dies, the Cerritos is tasked with preparing his collection to be catalogued. The new chief of security, Kayshon, joins the away team with Mariner, Tendi, Rutherford, and Jet Manhaver, an ensign who takes over Boimler's position and makes Mariner feel threatened. Meanwhile, on the Titan, Boimler helps an away team survive a dangerous mission but is accidentally cloned when he is being transported back to the ship. Unknown to starfleet Collector Siggi steals a rare mask, whereupon the dead collector's automated ship goes into lockdown and attacks the away team as they try to escape. Kayshon is turned into a rag doll in the chaos. Freeman does not check in with the team following a leadership review that criticized her for micro-managing. Manhaver and Mariner clash over their different approaches to escaping, before realizing that they need to let Rutherford and Tendi take charge. They make it back to the Cerritos, where Boimler is now assigned to separate him from the clone that stays with the Titan.
3 "We'll Always Have Tom Paris"
Chief medical officer T'Ana sends Tendi on a mission to retrieve an important family heirloom, and Mariner joins her. After retrieving an old box, they decide to look at what is inside and find a "libido post" that Caitians like T'Ana use to relieve their annual need to have sex. The pair accidentally break the post and are unable to fix it, with Tendi returning it to T'Ana broken. The doctor says that she only wanted the box anyway. Rutherford is startled to see tactical officer Shaxs walking around the Cerritos after Shaxs had sacrificed his life to save Rutherford. He is assured that members of Starfleet's bridge crews die and return in many different ways quite often, but still wants to know how Shaxs survived. When he finally builds up the courage to ask, Shaxs tells him something so horrifying that Rutherford is scarred forever. When Lieutenant Tom Paris boards the ship, Boimler wants to meet him and have Paris sign a commemorative plate with his face on it, but due to access issues he has to crawl through the Jefferies tube to get to the bridge.
4 "Mugato, Gumato"
When a rare Mugato is detected on a planet that it should not be on, the Cerritos is sent to investigate. Mariner, Boimler, and Rutherford join Shaxs and the away team, but not before Boimler and Rutherford learn from the Cerritos bartender that Mariner may be a Section 31 spy. The team discovers many Mugatos that are being kept captive by Ferengi, who are harvesting and selling the animals' horns. The away team attacks and the Mugatos are released, but Boimler and Rutherford get lost in the chaos. The Ferengi's buyer attempts to escape and is captured by the Cerritos, which accidentally destroys his ship. Freeman compensates him with a shuttle and some valuable items, before learning that this was a scam. Boimler and Rutherford find Mariner and she convinces them that she is not a spy. Together they convince the Ferengi to change their operation into a Mugato sanctuary and profit off visitors. On the Cerritos, Tendi is tasked with tracking down and scanning crew members who have been avoiding their regular medical checkups.
5 "An Embarrassment of Dooplers"
The USS Cerritos heads to Starbase 25, escorting a Doopler emissary. Dooplers are a species that involuntarily duplicate when embarrassed. The crew are strained to make him comfortable, but look forward to enjoying a Starfleet afterparty being held at the starbase. Boimler continues to describe his time on the USS Titan to Mariner's annoyance, but she hatches a plan for the two of them to sneak into the afterparty using Boimler's clone's invitation. Meanwhile, Tendi and Rutherford work on rebuilding a favorite model ship of theirs, but Rutherford is frustrated that he cannot rebuild it with seemingly the same ease as his earlier self. Captain Freeman accidentally embarrasses the Doopler emissary, causing him to uncontrollably duplicate throughout the ship as they arrive at the starbase. At the party, only Boimler is allowed in, causing Mariner to reiterate her feelings that Boimler abandoned her to work on the Titan. He leaves the party to join her at a dive bar on the base and they reconcile. Tendi reveals to Rutherford that the ship model was made to be incomplete by his former self so that the two could continue spending time together, and she reassures him that he is himself. Captain Freeman realizes that the Doopler can pull himself together if he is angered and orders the crew to insult him until he coheres. She and the senior officers head to the afterparty, but find themselves shut out and ignored by the other captains. Mariner invites them to the dive bar, where they all discover that Kirk and Spock once drank there, too. The crew celebrates together, with Mariner and Boimler carving their names in the bar alongside Kirk and Spock's.
6 "The Spy Humongous"
The USS Cerritos takes in a Pakled refugee, but come to suspect him of being a spy, albeit an inept one. Captain Freeman orders Commander Ransom and Lieutenant Kayshon to keep him busy, while she attempts to negotiate a ceasefire with Pakled leadership. Meanwhile, the lower deck crew have been assigned anomaly consolidation duty, cleaning up dangerous and unpredictable mission anomalies left over by the crew. Tendi attempts to keep positive despite Mariner and Rutherford's disdain, while Boimler is invited to join a group of red shirts. The group have ambitions of obtaining higher ranks, styling themselves after captains, and are interested in Boimler's Titan experience. They give Boimler a makeover and urge him to distance himself from the other lower deck members. As the work becomes taxing, Tendi merges with an artifact feeding off of her frustration, turning her into a large scorpion-like creature that runs rampant through the ship. While the red shirts do nothing but pontificate to prove their crisis leadership skills, Boimler takes action to make Tendi laugh at his own expense, freeing her from the artifact's influence. The red shirts express distaste for Boimler making a fool of himself, but Boimler tells them that their pretenses are a waste of time, and that true captains take action to help their friends and crew. During negotiations, the spy returns from the ship and Freeman is able to get him to reveal that they plan to attack Earth with a Veruvian bomb. Meanwhile, the lower deck crew use a submanifold casting stone they recovered during their cleanup to prank call Armus.
7 "Where Pleasant Fountains Lie"
The USS Cerritos is hailed by Queen Paolana, ruler of Hysperia, a Renaissance-styled society from a planet colonized by fantasy enthusiasts. She asks her son, Lieutenant Commander Andarithio Billups, to help fix an issue with engines of their ship, the Monaveen. Billups reluctantly agrees, wary of his mother's repeated attempts to lure him back to the kingdom from Starfleet by attempting to have him lose his virginity, which, by Hypserian tradition, would result in him ascending to the throne as king. Meanwhile, Boimler is disappointed after he is reassigned from an exciting field mission to instead join Mariner in escorting a malevolent computer AI named AGIMUS to the Daystrom Institute for study. Their ship is caught in an anomaly and crash lands, stranding them on a desert planet, unable to send a distress signal. AGIMUS offers to assist them if they will connect him to an available computer, but they refuse. Billups and Rutherford work on the Monaveen's engines, but Billups witnesses the engines explode, seemingly killing Rutherford and Paolana, and forcing him to ascend as king. Tendi is devastated by Rutherford's death, but locates his cybernetic implant signaling aboard the Monaveen and realizes that he and Paolana are alive, and the explosion was a ruse by Paolana to get Billups to return to Hysperia. Rutherford is able to stop Billups from losing his virginity to Paolana's sexually-trained Hysperian Royal Guards in time, and Billups returns to the Cerritos. Meanwhile, with the situation dire, AGIMUS attempts to sow discord between Mariner and Boimler, revealing that she had him reassigned, as she did not believe he was capable of the field mission. Boimler fights and incapacitates Mariner and connects AGIMUS to a deserted ship's computers, where AGIMUS revels in its new plans to take over the system with its returned access. However, Boimler reveals that he tricked AGIMUS, and merely used its battery to send a distress signal, knowing it can't be trusted. As they are rescued and AGIMUS is deposited at the institute, Mariner is impressed at Boimler's savvy and apologizes for getting him reassigned.
8 "I, Excretus"
Friction between the members of lower decks and the senior officers grows when the lower decks members are accidentally left behind in space following a spacewalk repair mission. A Pandronian drill instructor Shari yn Yem arrives from Starfleet to oversee a series of holodeck drills on the USS Cerritos to build better understanding between the crew, first by having the lower decks members switch responsibilities with the senior officers. However, the entire ship's crew fail their assigned drills, with the exception of Ensign Boimler, who achieves high marks in his Borg drill, but obsessively reruns the drill in an attempt to achieve a perfect score. Conflict comes to a head when Mariner and Captain Freeman's disagreements cause the team to fail a simple docking drill in record time. Their failure causes them to better appreciate one another, and they come to suspect that the drills were rigged for failure, believing this was Shari's plan all along to bring them together. However, Shari reveals that the rigged drills were actually a bid to ensure her continued employment with the Federation, and that she plans to send the Cerritos's failed scores to prove her necessity, which will likely result in the ship's decommission. Realizing that Boimler is the only crew member still running an active drill, they tell him to stall the drill to prevent the scores' finalizations. While Boimler runs through the drill again, Freeman has the crew fly into a series of dangerous situations, terrifying Shari, and demonstrating that the crew are more than capable and that Shari's drills aren't informed by real world experience. Freeman threatens to continue putting the ship through these runs until Shari changes their score to passing, which she does. Afterward, Freeman and the senior officers apologize to the lower decks members by providing them with a senior officer food replicator.
9 "wej Duj"
The USS Cerritos goes on a 12-hour warp, allowing the crew a day of rest, but Ensign Boimler finds himself as the only one of his friends to lack a bridge member to spend time with. Encountering Commander Ransom and his group of friends, all from Hawaii, Boimler lies about being from Hawaii as well to gain their friendship. Meanwhile, aboard a Klingon Bird of Prey, the Che'ta, lower decks officer Ma'ah hopes to rise to second officer to Captain Dorg. On a Vulcan cruiser, the Sh'Vahl, lower decks officer T'lyn comes into conflict with her captain and fellow crew when her work and her emotional reasoning step outside the prescribed tasks at hand. T'lyn detects an anomaly in the sector and, despite her also urging her captain to investigate based on her instincts, her captain acquiesces to her sound logic. Ma'ah gains Dorg's respect and accompanies him to a meeting with the Pakleds. He is disturbed to learn that Dorg has been supplying the Pakleds with weapons and Veruvian bombs that they intend to use against Earth. Dorg hopes to instigate a war and come to glory over their allies and enemies. The Pakleds' testing of the Veruvian bombs has caused the local anomalies. The Cerritos detects the anomalies and drops out of warp, encountering the Pakleds and the Che'ta, which attack. During the assault, Boimler confesses to Ransom that he isn't Hawaiian, but Ransom and the others reveal they also lied and just enjoy each other's company. The Cerritos is saved by the arrival of the Sh'Vahl. Aboard the Che'ta, Ma'ah challenges Dorg's dishonorable use of the Pakleds and his insubordination of the Klingon High Council's wishes, killing him in battle and becoming captain. He orders the Che'ta to retreat to the Klingon home world. The Pakleds flee. Despite turning the tide of the battle, T'lyn is punished for her continued emotional transgressions by being transferred to a Starfleet ship. Aboard the Cerritos, Ransom recommends Boimler to assist a young ensign. Boimler gladly mentors him, emphasizing that the heart of the ship is its lower decks.
10 "First First Contact"
The Cerritos is assigned to assist the USS Archimedes under Captain Sonya Gomez ("Q Who," "Samaritan Snare") in a first-contact mission. However, a solar flare results in the Archimedes losing power and being pulled into the planet's gravity well. With only 20 hours in which to work, Freeman must galvanize the crew into making modifications to the Cerritos that will allow her to close with the Archimedes and stabilize her with a tractor beam. Compounding the problem is the fact that Freeman has been offered a promotion, which will take her off the Cerritos while everyone else stays behind; Mariner, overhearing and with her fear of abandonment rearing its ugly head, spreads the word to the senior staff, who begin to bicker with Freeman. Tendi learns that she is being removed from Sickbay staff and begins to fret. Finally, Rutherford begins having trouble with his cybernetic implant, which is running out of storage space: he admits to Billups that he makes triple redundant backups of his memories of Tendi, unwilling to lose their friendship again. The day culminates when Boimler, in Cetacean Ops, flips the switch on the final modification, allowing the Cerritos saves the Archimedes. Tendi learns that she's being promoted to the Sciences division, as Dr. T'Ana feels her potential is wasted in Sickbay. Rutherford, deleting his redundant memories, receives a flashback which suggests his cybernetic implant was installed against his wishes. Lastly, Freeman is arrested for detonating a Veruvian bomb on Pakled Planet; the crew, gathered to wish her well in her promotion, must instead witness her being taken away manacled.