This episode is generally a reference to TOS 1x03: Where No Man Has Gone Before, where a man named Gary Mitchell gains new abilities after he is exposed to “strange energies”. Doctor T'Ana mentions Gary shortly after diagnosing Ransom.

Minor references:

• The opening scene in the Cardassian interrogation chamber as well as Boimler's quote “They keep showing me lights!” are referencing TNG 6x10 & 6x11: Chain of Command where Picard was subjected to physical and psychological torture at the hands of the Cardassians.

The collectors and their attempts to collect Commander Data are a reference to the TNG episode TNG 3x22: The Most Toys.

Kayshon is a Tamarian. Their species first appeared in TNG 5x02: Darmok, where Picard first discovered that their language is based on metaphor. Kayshon utters several lines from that episode.

The various references to Will Riker's transporter-clone are from TNG 6x24: Second Chances.

At the end of the episode, Jet Manhaver is suddenly seen wearing lieutenant's pips, but he brushes one of the pips away and explains that it was just a piece of corn. He says “Half the time when you see someone with the wrong amount of pips around here, it's usually just delicious street corn!” This pokes fun at the numerous times across the entire Star Trek franchise where officers were seen with the wrong rank insignia. Jet, himself, was seen with lieutenant's pips in Season 1, along with Shaxs who sometimes incorrectly wore commander's pips.
Other notable characters who wore incorrect insignia include Chief O'Brien in TNG, Lieutenants Paris, Torres, and Tuvok in VOY, and Valeris from Star Trek VI: The Undiscovered Country.

Minor references:

• Regarding the away team's late arrival, Siggi says “What'd you do, stop to debate the human rights of a robot?” This is a reference to TNG 2x09: The Measure of a Man, where Data's rights as an individual were litigated.
• There are a ton of easter eggs among the collector's collection – I will only point out some of them...
  • Shortly after arriving on the collector's ship, Mariner briefly picks up some sort of headset and then places it back onto an orange-colored bust. The headset is the addicting game that took over the Enterprise‑D in the aptly named episode, TNG 5x06: The Game. The bust is a likeness of Captain Jean-Luc Picard, sculpted by one of the children on the Enterprise‑D for “Captain Picard Day”, as seen in TNG 7x12: The Pegasus.
  • Rutherford inventories “another old disintegrator”. Worf used one of these weapons in Star Trek: Insurrection.
  • The gigantic skeleton wearing a tattered blue Starfleet uniform is ostensibly that of Spock Two, from TAS 1x07: The Infinite Vulcan.
  • When escaping from the flying vacuum cleaners, the gang hide in a diorama featuring the remains of two Excalbians, with one having taken the form of Abraham Lincoln and still wearing his stovepipe hat. These aliens were from the TOS episode TOS 3x22: The Savage Curtain.
• When starting to bond with the newly-duplicated Boimler, Riker asks the computer to play “Night Bird”. This is another nod to the episode TNG 6x24: Second Chances, where Riker was unable to perform the trombone solo from the piece.

Robert Duncan McNeill reprises his role as the titular character, Tom Paris from Star Trek: Voyager.

Minor references:

• The title of this episode is a play on the famous line, “We'll always have Paris” from the 1942 film Casablanca. There's an unrelated TNG episode also named after the line, TNG 1x24: We'll Always Have Paris.
• When Boimler brings up Tom Paris, Mariner asks “Is he still a salamander?” and Boimler mentions that Tom was the first human to break the trans-warp barrier. These are references to arguably the worst episode of Voyager, VOY 2x15: Threshold where Tom travels at Warp 10 and then... well, he... turns into a salamander.
• Boimler and Mariner list off a few possible ways that Shaxs could have come back from the dead...
  • Boimler suggests a “transporter pattern buffer thing”, likely referencing Scotty preserving himself in a transporter pattern buffer for 75 years in TNG 6x04: Relics.
  • Mariner suggests a restored katra, and Boimler says he could have been “Genesis Deviced”, both referring to Spock's restoration in Star Trek III: The Search for Spock.
  • Then Mariner suggests a Mirror Universe switcheroo, referencing characters from Star Trek: Discovery who were replaced by their alternate universe counterparts, such as Spoiler » Phillipa Georgiou.
  • Next, she suggests that the Borg may have rebuilt him, probably referencing Neelix's restoration using Borg nanoprobes in VOY 4x12: Mortal Coil.
  • Boimler says he could be a “future son from an alternate timeline”, likely referencing Tasha Yar's daughter, Sela, who was revealed in TNG 5x01: Redemption II.
  • The “time ribbon” or “Nexus” (same thing), refers to Star Trek: Generations. Later, one of the Shaxs hallucinations that Rutherford experiences says “It's always Christmas in the Nexus!” which refers to Picard's initial experience in the ribbon.
• Boimler breaks the fourth wall by humming the theme song to Star Trek: Voyager while walking through the corridor.
• Tendi asks if the band playing on the speaker is “Gik'Tal”, which is Klingon for “to the death.” The song is called “Gre'thor Paradise”. Gre'thor is the Klingon version of “Hell”, where the souls of the dishonored go after death.
• Mariner plays dom-jot with a group of Nausicaans at Starbase Earhart. This is where – and how – Jean-Luc Picard ended up in a fight where he was stabbed through the heart, as told in the episode TNG 6x15: Tapestry.

These horned ape-like creatures called mugato or gumato were first seen in TOS 2x19: A Private Little War. The title of this episode is a reference to the common idiom “Tomayto, tomahto” and pokes fun at the fact that there are several names for these creatures mostly because the actors in the original TOS episode couldn't consistently pronounce the name correctly.

Minor references:

• In the teaser, Mariner, Boimler, and Rutherford play anbo-jyutsu. This sport was only ever seen once before, in TNG 2x14: The Icarus Factor.
• Mariner asks the Ferengi if they're “some creepy throwback Last Outpost-style Ferengi”. She is referencing the very first appearance of Ferengi in the Star Trek franchise, in TNG 1x05: The Last Outpost, where they were definitely strange, annoying creatures.

Minor references:

• Malvus says that Mariner stranded him on Ceti Alpha IV, which is even worse than Ceti Alpha V. Ceti Alpha V is where Kirk left Khan in TOS 1x22: Space Seed, to be found again years later in Star Trek II: The Wrath of Khan.
• Boimler says that Mariner once stranded him on Rubicun III. That's the planet with the libidinous population that administers the death penalty for simple infractions, first seen in TNG 1x08: Justice.
• Regarding the Commander Data bubble baths, Malvus admits some of them might be “Lores”. Lore is Data's identical evil twin brother, first seen in TNG 1x13: Datalore.
• Boimler yells “fish people!” during the buggy chase. Those are Antedians, who first played a very minor role in TNG 2x19: Manhunt.
• At the party, Boimler points out Captain Shelby and her number one. Shelby is originally from TNG 3x26 & 4x01: The Best of Both Worlds, and her number one resembles the terrifying early concept for the Kelpien race from Star Trek: Discovery. Boimler next points out Captain Exley and his number one, neither of whom have ever been seen before in Trek.
• There are a few easter eggs at the bar where Mariner and Boimler end up. On the top shelf behind the bar, there's a model of the Guardian of Forever portal from TOS 1x28: The City on the Edge of Forever. Sitting on the bar is a model of Earth's first warp-capable ship, the Phoenix, from Star Trek: First Contact. Mounted above the bar is a model of the Planet Killer from TOS 2x06: The Doomsday Machine. There are some more references in the paintings on the walls, but I'm not going to list them all here.
• When hearing that the DJ at the party is Okona, Freeman says “This is outrageous!” Okona is a roguish man from the episode TNG 2x04: The Outrageous Okona.
• Regarding the model of Deep Space Nine, Rutherford is excited to see that it comes with an Ezri and a Jadzia. You're just going to have to watch all of Star Trek: Deep Space Nine to appreciate that line.

At the end of the episode, the gang “prank calls” Armus. Armus is the black-tar-looking creature encountered by the Enterprise‑D crew in TNG 1x23: Skin of Evil.

Minor references:

• The Pakleds keep calling Freeman “Janeway”, confusing her with the captain of the USS Voyager from Star Trek: Voyager.
• Virtually none of the items that Mariner, Rutherford, and Tendi collect during anomaly consolidation duty are any kind of reference to anything previously seen in Star Trek.
• Boimler hesitantly asks his new friends about calling themselves “redshirts”. This is a bit of a fourth-wall-breaking joke from The Original Series when security officers used to wear the red uniforms. Fans gave the term “redshirts” to the extras playing security officers who always seemed to die in unproportionate numbers.
• Rumdar's request to see the “crimson forcefield” is a reference to a ruse used by the Enterprise‑D crew during the Pakleds' first appearance in TNG 2x17: Samaritan Snare.
• When Boimler delivers his inspiring speech, he imagines himself on the bridge of a Galaxy-class starship, like the Enterprise‑D from Star Trek: The Next Generation, the ship most-commonly associated with William Riker.

The evil AI, AGIMUS, is voiced by veteran Trek actor Jeffrey Combs, who has played numerous roles in the past, including Brunt and Weyoun in Star Trek: Deep Space Nine and Shran in Star Trek: Enterprise.

Minor references:

• Mariner suggests burying AGIMUS “like Data's head”, referencing TNG 5x26 & 6x01: Time's Arrow.

Alice Krige reprises her role as (a holographic version of) the O.G. Borg Queen, originally from Star Trek: First Contact.

Mariner's first simulation involves the Mirror Universe, first seen in TOS 2x04: Mirror, Mirror. The Mirror Universe was also seen in DS9, ENT, DIS, and PRO.

Tendi's simulation about navigating a paralyzed Klingon's request for an honorable death is a direct reference to TNG 5x16: Ethics.

Mariner's “Old West” simulation references TOS 3x06: Spectre of the Gun.

Rutherford's simulation about fixing the warp core to save the ship is a reference to Star Trek II: The Wrath of Khan.

Boimler's Borg simulation doesn't seem to reference any particular Borg encounter, but the “babies in a drawer” concept is from the very first Borg episode, TNG 2x16: Q Who. Boimler is later assimilated, becoming “Excretus of Borg”, referencing “Locutus of Borg” from TNG 3x26 & 4x01: The Best of Both Worlds.

Mariner's “Naked Time” simulation comes from the episode TOS 1x04: The Naked Time, although the TOS episode was more about bearing “naked” emotions, not literal nudity.

The joint test about stealing the Cerritos from spacedock to save Spock is a reference to Star Trek III: The Search for Spock.

Mariner finds several crystalline entities in the ship's vicinity. The original crystalline entity was first seen in TNG 1x13: Datalore.

Minor references:

• The test instructor is a Pandronian, a species first seen in TAS 2x02: Bem.
• Other test titles seen on various displays include:
  • “Carbon Based Units”, likely referencing the Ilia probe in Star Trek: The Motion Picture.
  • “Cause & Effect”, likely referencing TNG 5x18: Cause and Effect.
  • “Chain of Command”, likely referencing TNG 6x10 & 6x11: Chain of Command.
  • “EMH TAK--” (the rest is cut off), likely referencing the Emergency Medical Hologram from Star Trek: Voyager.
  • “Escape the Void”, likely referencing VOY 7x15: The Void.
  • “Evolution”, likely referencing TNG 3x01: Evolution.
  • “Extreme Engineering”, which doesn't seem to reference anything specific.
  • “From Q to Q”, referencing the Q entities, but not any particular episode.
  • “Hero Worship”, likely referencing TNG 5x11: Hero Worship.
  • “Kobayashi Maru”, referencing the Academy simulation designed to test a cadet's ability to handle a no-win situation, first seen in Star Trek II: The Wrath of Khan.
  • “Natural Selection”, which doesn't seem to reference anything specific.
  • “Survival of the Fittest”, which doesn't seem to reference anything specific.
  • “Teleportation Death Tag”, which doesn't seem to reference anything specific.
  • “The Tholian Web”, likely referencing TOS 3x09: The Tholian Web.
  • “Time Loop”, referencing any number of similar phenomena in Trek.
  • “Time Trap”, likely referencing TAS 1x12: The Time Trap.
  • “Tribble Infestation”, which doesn't seem to reference anything specific.
  • “Tribble Troubles”, likely referencing TOS 2x15: The Trouble with Tribbles.
  • “Whale Rescue”, likely referencing Star Trek IV: The Voyage Home.

Minor references:

• During their time off, Boimler suggests a strategema tournament. Strategema is a tabletop game originally seen in TNG 2x21: Peak Performance.
• While Tendi and Dr. T'Ana are rock climbing, Boimler joins them wearing rocket boots and a shirt that says “Go climb a rock.” These are references to the opening scenes of Star Trek V: The Final Frontier.
• Mariner and Freeman argue while playing a game of velocity on the holodeck. The game was first seen when Captain Janeway and Seven of Nine played it in VOY 4x26: Hope and Fear, and they also used the game as a forum for airing their disagreements.
• At one point, Boimler fears that he could be demoted to work at a penal colony where he'd “have to mate with the enemy to form a new civilization...”. This is possibly a reference to TNG 6x17: Birthright, Part II, where some Romulans were obligated to oversee a penal colony holding Klingon survivors of Khitomer, and the two populations began to intermarry.
• Ma'ah says, “Klingon blood runs as reddish-pink as ever!” This lightly pokes fun at the inconsistency in the color of Klingon blood over the franchise's history. Originally shown as red in TNG, Klingon blood was famously depicted as opaque pink in Star Trek VI: The Undiscovered Country, much the same way that it is depicted in this Lower Decks episode. Fans have long theorized that the shift to pink blood was made to avoid a higher MPA rating for the film (PG-13 or R), but other fans recount stories of film director Nicholas Meyer stating that the pink color was purely an artistic choice, used to highlight a big reveal toward the end of the movie.
• Before beaming over to the Pakled ship, Captain Dorg says “Cry ‘Havoc!’ and let slip the dogs of war!” This line from Shakespeare's Julius Caesar (Act III Scene 1) was also once famously uttered by General Chang in Star Trek VI: The Undiscovered Country.
• While playing a futuristic version of the board game Clue, Mariner mentions a sniper rifle that can shoot through walls. This is a reference to DS9 7x13: Field of Fire.

Lycia Naff reprises her role as Sonya Gomez. Now captain of the USS Archimedes, Gomez was first seen as a young ensign in engineering on two episodes of TNG, TNG 2x16: Q Who and TNG 2x17: Samaritan Snare. When an ensign trips and falls on the bridge, Captain Gomez says she's “done way worse in front of much more intimidating captains”. She's talking about spilling a cup of hot chocolate on Captain Picard in the episode “Q Who”.

Minor references:

• Boimler prepares for Captain Freeman Day, referencing Captain Picard Day from TNG 7x12: The Pegasus.
• After learning about Freeman's promotion, Mariner fears ending up with “some weirdo with a riding crop”, referencing Captain Styles from Star Trek III: The Search for Spock.
• Tendi mentions the “rubber duckie room”, which is a meta-reference to designer Michael Okuda, who hid a drawing of a small rubber duck in one of the rooms on the master systems display (MSD) for the Enterprise‑D in TNG. There is a similarly-marked room on the MSD on the Cerritos.