The title refers to the legendarily controversial VOY episode “Tuvix”, which is still so divisive in fandom today that discussions on it are tightly regulated, if not outright banned, in some fan forums.
Boimler is put on holodeck waste disposal duty, removing all the organic material caught in the biofilters after holodeck sessions. It is a particularly odious chore that Mariner performed in LD: “Moist Vessel”. T’Lyn remarks that Boimler’s odor will be repulsive - Vulcans are known to find the smell of humans oppressive even under the best of circumstances, and some take nasal suppressants/numbing agents (Spock in SNW: “Charades”, T’Pol in ENT: “The Andorian Incident”) while getting used to it. Female Vulcans have more sensitive senses of smell than males.
The Portelo space station is a redress of the Regula-I type station first seen in ST II, with drydock facilities attached. The original was the orbital station model at the start of TMP turned upside down. The Regula I model has been reused in TNG, VOY and LD and we’ve seen a better armed variant of it in DS9.
Beljo Tweekle (named after the original superfan Bjo Trimble?), from his facial markings, is a native of Rigel V (ENT: “Affliction”). LT Drew Pratchett, of the USS Oakland, is also a Rigelian (LD: “Much Ado About Boimler”).
In the titles, the increasingly crowded battle between the Crystalline Entity, the Romulans, the Borg, the Klingons and the Pakleds is now joined by the Whale Probe (ST IV) and what I think is a Breen warship.
This episode takes place on Stardate 58724.3, which is c. 2381. Freeman mentions that Voyager will spend some time on the surface of Earth before being moved to orbit. The Intrepid-class was specifically designed to be able to perform a planetary landing and takeoff (VOY: “The 37s”).
By 2401, the Voyager will be on display at the Fleet Museum orbiting Arthan Prime (PIC: “The Bounty”). However, the ship at the museum has some differences from the original (and this restored version), most notably the prominence of the hull plating and the lack of a name and registry number on the underside of the primary hull.
The mannequin that Boimler drops is that of ENS Harry Kim, from the hairstyle. Tweekle calls it a “mission-worn uniform”, much like the “screen-used” props and uniforms that are occasionally auctioned off. Rutherford refers to the time when an alien cheese infected the bio-neural gel packs of Voyager’s computer system (VOY: “Learning Curve”).
Kayshon says, “Unzak, when he guided the florkas to their roost.” Florkas are small green winged insects used by Tamarians who are trying to ascend to a higher plane of existence (“Moist Vessel”).
T’Lyn says Voyager is outdated and smells like Borg (how does she know what they smell like?). The ship did have an inordinate number of encounters with the Borg, and of course the ex-Borg Seven of Nine served on board. The storage cylinder Tendi holds contains the infamous orchid that caused the Tuvix incident.
Like all Cerritos shuttles, the Yosemite II is named after a United States National Park. The original Yosemite appeared in several episodes before it crash landed and was considered unsalvageable in LD: “Where Pleasant Fountains Lie”. The current shuttle first appeared in LD: “Grounded”.
T’Lyn says she enjoys an accurate label. That woman is out of control.
When T’Illups materializes on the pad, they are wearing clothes with the same swirly floral pattern that Tuvix had on their “combined” uniform. Mariner isn’t wrong when she says Janeway “straight up” murdered Tuvix - the argument is whether she was right in doing so.
The creature Mariner releases is a macrovirus (VOY: “Macrocosm”) that once infected Voyager in 2373. While Janeway managed to lure what she thought was all of the virus to the holodeck and eliminated them with an antigen bomb, obviously she missed at least one.
Mariner mentions the “Pike Thing” they aren’t supposed to talk about (SNW: “Those Old Scientists”), possibly placing that episode between the events of Seasons 3 and 4.
Shax asks about T’Illiups’ “physical memories” as he and T’Ana are romantically involved. In the corridors of Voyager we see an exhibit with two mechanical salamander creatures (VOY: “Threshold”).
Chaotica (VOY: “Night”, et al.) and Michael Sullivan (VOY: “Fair Haven”) are holodeck programs on Voyager. The Clown is actually from an alien simulation (VOY: “The Thaw”) and was never actually hooked up to Voyager’s holodeck (as Mariner points out).
Tweekle says he installed holo-emitters all over the ship, like the Hirogen did when they took over Voyager (VOY: “The Killing Game”). The USS Prometheus also had shipwide holo-emitters.
Tweekle’s remark about “subtle updates that don’t impact historical consistency are an acceptable compromise for conservation” may be a reference to the updating of VFX in the remastered versions of TOS, as well as the visual updates in various Star Trek shows, notably DIS and SNW. This explains the presence of the Clown in the database. Sullivan kisses Mariner - he was Janeway’s character’s love interest in the “Fair Haven” simulation.
Harry’s clarinet is embedded in the macrovirus that topples the Borg regeneration alcoves, and it then picks up a stray nanite (as does one of the salamanders), probably one of Seven’s.
The entry on Freeman’s PADD about Tuvix is stardated 49678.4, the of the second log entry in “Tuvix”, two weeks after Tuvix was created.
Shax has been merged with Ops officer ENS Barnes to create Shabarnes. T’Illups orders that Honus the bartender be merged with Transporter Chief Lundy to create Chondus. An unconscious LT-CMD Steve Stevens is also dragged out with an unknown blonde female officer. Stevens is merged with Matt the Whale from Cetacean Ops to create Swhale Swhalens.
On Voyager, the Borg-Salamander sets a course for Borg Cube 858779. Sullivan holds Ransom, Kayshon and Rutherford captive in Voyager’s Astrometrics lab. Sullivan sighs that he misses his wife - in a notorious scene from “Fair Haven”, Janeway, to advance her romance with the married Sullivan, tells the computer to “delete the wife”. While Janeway banned herself from altering his program again, as far as we know she never restored Frannie, so it’s not explained why Sullivan even remembers her.
Boimler claims he is the son of Captain Proton, who was of course Tom Paris’ character and Chaotica’s arch-nemesis in the simulations. Rutherford uses the alien cheese to break Voyager’s bio-neural systems.
The California-class starship seal displayed behind Freeman at the promotion ceremony has the color scheme and the bear from the state flag of the Republic of California, combined with a California-class silhouette above the state motto “Eureka!”
Boimler, Mariner Tendi are promoted to LT j.g. and T’Lyn to Provisional LT j.g. Rutherford is left out because he “broke” Voyager, even if it was for a good cause.
The Klingon Bird of Prey is the IKS Che’Ta’, last seen in LD: “wej Duj”, commanded by Captain Ma’aH. The Klingon spear is a gin’tak, first seen in TNG: “Redemption”. Ma’aH gives the order, “Destroy those qoHpu’!” qoH means “fool” and -pu is a suffix meaning people, so it literally means “foolish people” or just “fools”.