'''Season 1, Episode 10''':
!They've Got A Secret

The crew of Moya are sweeping the ship for any more Peacekeeper devices that might allow Crais to track them. D'Argo discovers one, but in trying to disable it, manages to blow himself out into space and release a strange cloud of bio-mechanical particles into Moya's systems. She soon reacts strangely, throttling the life support to the symbiont Pilot, and the atmosphere for her humanoid crew.

Crichton, Aeryn, Rygel and Zhaan must discover what has happened, restore Pilot and the life support, and deal with an amnesiac D'Argo who sees his shipmates as people from his hidden past...

----
!Tropes present in this episode include:
* ApopheniaPlot: Based on all the evidence, (malfunctions, [=DRDs=] going berserk, Moya getting aggressive, etc) Crichton theorizes that Moya's come down with some kind of biomechanoid virus - though even Aeryn remarks that this is a bit of a hasty conclusion to jump to. At the end of the episode, [[MistakenForDisease he's proved wrong]]: Moya is ''pregnant.'' All the malfunctions were due to her diverting power to her offspring; the [=DRDs=] got aggressive because Crichton was trespassing on an area dangerously close to her baby; Moya [[MamaBear became violent]] because the crew resisted her efforts to keep her child safe and [[PoorCommunicationKills she had no way of communicating what was happening]].
* BatmanGambit: To get D'Argo to snap out of it, Crichton and Zhaan deliberately play their respective parts, complete with "Lo'Laan" expressing impending dread and "Macton" denouncing his brother-in-law. The building anger pushes D'Argo to the realization of what's really happening.
* BizarreAlienBiology: Especially pronounced this early in the show. D'Argo can survive for up to fifteen minutes in the vacuum of space. And more importantly, Moya is pregnant, because she can reproduce via some sort of parthenogenesis.
* BruiserWithASoftCenter: Behind all of his anger and lack of trust in his shipmates, D'Argo is revealed to have once been a HappilyMarried family man and now a HeartbrokenBadass both mourning his dead wife and worrying about the well-being of his missing son.
* CainAndAbel: Zhaan expresses surprise over Macton murdering his own sister.
* ContinuityNod: Crichton observes Aeryn might still have [[Recap/FarscapeS01E09DNAMadScientist remnants of Pilot's DNA]].
* DaddyHadAGoodReasonForAbandoningYou: D'Argo knew full well what Macton and other Peacekeepers would do to a hybrid child like Jothee, but leaving a young, confused son to fend for himself gnaws at him.
-->'''D'Argo:''' Jothee, please understand, I had to send you away. I was charged with your mother's murder. Before they arrested me, I got you to another planet safely away to a place where I prayed that Macton and others like him would never find you. I had no other choice, but I can't be sure you have remained safe until I see you again.
* DarkSecret: The truth about D'Argo's imprisonment is revealed.
* EveryoneHasStandards: Despite his earlier frustration with all this, Rygel looks quite sympathetic when D'Argo explains his fears over leaving Jothee to fend for himself at a young age.
* ExplainExplainOhCrap:
-->'''Crichton:''' Macton was a Peacekeeper?\\
'''Zhaan:''' If he was a Peacekeeper, then Lo'Laan was...
* {{Foreshadowing}}: D'Argo remarking that "Jothee" is starting to realize he looks different from the others and being treated as an outsider.
* InnocuouslyImportantEpisode: This episode is pretty important for D'Argo and Moya, but it also slyly sets up an element that relates to a [[Recap/FarscapeS02E05TheWayWeWerent later episode]].
* MalignedMixedMarriage: D'Argo was married to a Sebacean woman. Her Peacekeeper brother objected so strongly he ended up murdering her and framing D'Argo for it. Aeryn admits that Peacekeepers are indoctrinated to see unions with other species as "evil", although she assures D'Argo she doesn't view his son this way and will keep his secret.
* ManlyTears: D'Argo during the climax of his plot, as his memory fully returns.
-->'''Crichton:''' D'Argo, you have to remember.\\
'''D'Argo:''' ''[tearing up]'' I don't want to.
* MiscarriageOfJustice: D'Argo was framed the murder of his beloved wife and imprisoned by the Peacekeepers. He says Macton literally had Lo'Laan's blood on his hands when arresting him.
* MistakenForDisease: After witnessing Moya's biochemistry surging in baffling ways, machinery around the ship malfunctioning, and [=DRDs=] becoming aggressive towards members of the crew, Crichton initially believes that Moya has been infected by a biomechanoid virus left behind by the Peacekeepers. It's actually just the initial side-effects of Moya's pregnancy.
* OhCrap: Crichton when he realizes what Moya's been protecting so fiercely.
* RealAfterAll: Crichton is surprised when he learns the people D'Argo keeps talking about are real.
* TheReveal: D'Argo was married with a son and his "true crime", first mentioned in "Back and Back and Back to the Future", was that he was framed for the murder of his wife. Also, the reason Moya is acting strangely is because she's pregnant with a baby Leviathan.
* StopTheHeroTwist: Moya has seeming turned against the crew and they make the difficult decision to lobotomize her for their own survival. Then they discover that Moya is pregnant and just protecting her unborn child, and must call off the lobotomy over a poor-quality radio link.
* TragicKeepsake: D'Argo carries a device containing a holo-image of his wife and son.
* WhamLine: "Macton arrested me" for those who recall D'Argo saying he was arrested by a Peacekeeper.
* WhamShot: The holo-image of D'Argo's family.
** The shot of Moya's baby.
* WrongGenreSavvy: The crew come to believe that Moya is actively trying to kill them. Instead, she's just been diverting resources for her new baby.
----