From here on the episode consists of lengthy flashbacks interspersed with current events: we see Aeryn and Velorek arriving on Moya, with Pilot as the cargo of their ship. Velorek is a technical specialist in charge of bonding the new Pilot to Moya, while Aeryn has been pulled off Prowler duty to act as Velorek's personal chauffeur, which she is unhappy about. To add insult to injury, just seconds after Crais ignores her attempts to get herself reassigned, she's accosted by two other members of the firing squad, who mock "the high and mighty little Prowler pilot" for not helping them dig the Old Pilot's corpse out, and smear guts across her cheek for good measure.
In the present, Crichton finds Aeryn savagely beating a punching bag until her knuckles bleed. She breaks down in his arms and confides to him that she and Velorek were lovers. Normal Peacekeeper etiquette allows casual sex to fulfil physical needs, but strongly disapproves of emotional links; nevertheless, Aeryn felt something for Velorek that she now recognises as love.
And then, as if the situation couldn't get worse, Rygel gives Pilot the recording despite having previously agreed with everybody else that it should be hidden from him; Rygel claims that he felt morally obligated to do so, but the others suspect that he was looking to get one up on the rest with Pilot. Aeryn insists on going alone to speak to Pilot- and ends up getting half-throttled to death; D'Argo and Crichton come to her rescue and Pilot eventually calms down a bit, but refuses to move the ship any further until she leaves. With her relationship with Pilot in tatters and very little sympathy to be found among the crew, Aeryn is already packing her bags.
In flashback, we discover that Velorek, who'd been ordered to bond Pilot to Moya quickly by Crais, did so surgically rather than naturally, which has caused Pilot constant pain ever since. After making love to Aeryn, Velorek tries to get her to let him have them permanently posted together, and tells her that Crais is a maniac and that his project must be prevented; Aeryn accuses him of insubordination, and he again implores her to leave with him and unknowingly prefigures Crichton's later words to her: "You can be so much more".
Crichton goes to Pilot to plead on Aeryn's behalf. However, rather than carrying on with his accusations, Pilot reveals to him that Moya only accepted him because the Peacekeepers used the control collar to torture her into it, and in a fit of suicidal despair, he physically severs his connection with her, sending Moya's life-support systems into gradual shutdown and ensuring a slow death for himself. Aeryn insists on talking to Pilot again, but he has locked himself in the den and set the DRDs to fight off anyone who tries to enter. Aeryn and Crichton sneak in through the maintenance passages, but along the way, Crichton realises that Aeryn still hasn't told him the whole truth, and insists on it.
Aeryn reveals that Velorek and some of his men were plotting to sabotage Crais's "project," and though she didn't know what this project was at the time, she used this information to betray Velorek to Crais in exchange for being returned to Prowler duty, resulting in Velorek's execution. She explains that she now realises that the project was to breed a Peacekeeper-Leviathan hybrid battleship on Moya, and to prevent it, Velorek probably installed the contraceptive shield that D'Argo later accidentally broke- unknowingly completing Crais's plan and causing Talyn's conception.
Back in the present, Crichton and Aeryn arrive in the den: after a shootout with the [DRDs] and an angry standoff, Aeryn offers her life to Pilot, acknowledging that she deserves to die for what she did. Hower Pilot admits that he believes that he should be the one to die: he reveals that the elders of his people considered him too young to be bonded to a Leviathan, but that Velorek offered him the chance to do so without their authority. Desperate to see the stars and the universe beyond his home planet, he accepted it, even though he knew full well that it would mean the death of another Pilot. In the present, he believes that had he refused, Velorek would never have found a Pilot willing to accept his offer and that Moya's orginal Pilot might still be alive.
Aeryn remembers Velorek's compassion to Pilot when he first came aboard, which she didn't understand at the time and does now; stroking Pilot's cheek in much the same way Velorek did, she tells him that both of them have come a long way, but still have a long way to go together. Finally broken out of his suicidal depression, Pilot instructs D'Argo and the others on how to create a new link between him and Moya; this time, he will allow it to form naturally and painlessly, although it will take up to a cycle for him to regain full connection and control.
Alone with Crichton, Aeryn tells him that Velorek said exactly the same thing to her that he did: "You can be so much more." Crichton asks her again if she loved Velorek, and she agrees- with the heavy implication that she now has similar feelings for Crichton.
Tropes present in this episode include:
- Abuse Mistake: The audience experiences this when Velorek appears to be attacking Aeryn but it's revealed that they are actually lovers.
- The Atoner: both Aeryn and Pilot try their best to be this
- Be Careful What You Wish For: Aeryn's rather cold-blooded decision to barter her love in exchange for thirty pieces of silver - namely, to get back into space where she belonged. By her expression when Velorek is arrested, it's clear she regrets that decision. Ironically, Pilot was guilty of the exact same sin.
- Even more amusingly, had Aeryn gone with Velorek she never would have been accidentally captured by Moya, meaning in all likelihood she'd still be a Peacekeeper
- Bound and Gagged: In the second flashback in the episode, Pilot is transported aboard Moya wearing the Pilot equivalent of this- a covering of black netting and a steel gag.
- Call-Back: Aeryn deduces that Crais' ambition was to conceive Talyn, and that Velorek installed a Contraceptive Shield to thwart him. Since Velorek never broke under interrogation, and Crais could find no trace of sabotage, the counter-plot went off without a hitch... that is until D'Argo bungled his way into puncturing the shield last season.
- Call-Forward / Meaningful Echo: "You can be so much more"
- Continuity Nod:
- Aeryn undergoes another Samus Is a Girl moment.
- Zhaan taking Aeryn to task for her murder of a "defenseless creature." Aeryn responds by throwing the whole arm-cutting-off thing back in Zhaan's face.
- Aeryn recalls being implanted with Pilot's DNA.
- As congratulations for foiling Velorek's sabotage, Crais tells Aeryn to get in touch with Lieutenant Teeg (neck still unsnapped at this point, of course) for her new assignment.
- Cut the Juice: Inverted by Pilot, who yanks out his own guts to sever his connection with Moya, thus (in his own mind) "freeing" her.
- Deal with the Devil: The last flashback shows Velorek holding a conference with Pilot on his home planet of Doien. Velorek offers him a Leviathan, saying that the old Pilot will be killed no matter what he does; Velorek will just find someone else if he doesn't cooperate. Ergo, Pilot was voluntarily working with the Peacekeepers all along. He lived to regret his decision following the painful grafting process...
- Defector from Decadence: Velorek, unsuccessfully.
- Defiant to the End:
- According to Aeryn, Velorek never broke under his torture. Hence, Crais didn't know about the giant condom he installed.
- Also, the original Pilot refused to cooperate even when faced with a firing squad.
- Dr. Jerk: Following Pilot's near-strangulation of Aeryn, Zhaan is shown dabbing her neck with some tincture. When Aeryn flinches from its sting, Zhaan asks bitingly, "Did I hurt you, my dear?" Aeryn slaps her hand away and thanks Zhaan for her compassion.
- Et Tu, Brute?:
- Aeryn confesses that feels closer to Pilot than anyone else on the ship, not least because the pair of them share DNA. Pilot sneers, "That's why your betrayal cuts so deep."
- Subverted with Velorek. He's proud of her for having the initiative to make a deal with Crais, while most Peacekeepers would have evidently kept their heads down.
- Everyone Is Related: With the exception of Crichton, each of the principals were aboard Moya at the time of Velorek's hijacking three years ago. Aeryn momentarily crossed paths with a hooded Zhaan in the corridors, but took little notice of her.
- Flashback Effects: The film itself for the flashback scenes was processed using a technique known as bleach bypass to give them an aged look.
- In Medias Res: The Cold Open implies that the Peacekeeper jackboots have just seized Moya. In fact, they did — except it's in the past.
- Invulnerable Knuckles: Averted. Aeryn smacks her punching bag so hard, she knocks it off its pedestal, leaving her knuckles raw and bloodied.Crichton: You're making hamburger there.
- It's All My Fault: Pilot's revaluation ends up inverting this trope. Pilot's twinge of hate toward Aeryn was, in truth, directed at himself.
- Jitter Cam: used for the recording of the first Pilot's murder, as the cameras are meant to be attached to the Peacekeeper squad's helmets.
- Kicked Upstairs: Aeryn chafes at being diverted from Prowler detail in order to participate in some hush-hush project.
- Let Me at Him!: Crichton has to hold Aeryn back from attacking Rygel after being called a "Peacekeeper murderer."
- My Greatest Failure: Aeryn and Pilot both have blood on their hands. Aeryn's error is more poignant, as Velorek offered her the same chance as Crichton in the pilot episode; she made the opposite choice.
- Neck Lift: Pilot performs this on Aeryn- justified considering that he's a much larger creature.
- O.O.C. Is Serious Business: As noted by Crichton, Pilot would only offer snotty remarks over having his arm cut off, but he is positively pissed off here.
- Parodies for Dummies: When Pilot shuts off the power, Crichton laments that no one has a copy of Leviathans For Dummies.
- Please Kill Me If It Satisfies You: Aeryn says that she deserves to die, and won't stop Pilot from taking her life, but asks him to spare the others and himself.
- Posthumous Character: Tam Velorek.
- Punch a Wall: An actual punching bag, but with self-destructive intensity. The script originally called for Aeryn to punch a bulkhead, but Claudia Black reasoned that hitting Moya with her fists didn't play in the context of the scene.
- Retcon: this episode conflicts with Crais's apparent surprise at and lack of interest in the existence of Talyn when first finding out about his existence at the end of S1, although he might have just been hiding his knowledge from Scorpius.
- Either that, or like Aeryn, Crais didn't realize that Moya was the same leviathan until after boarding Talyn the first time.
- Scully Box
- SexFace Turn: Subverted.
- The title "The Way We Weren't" is a play on the 1974 film The Way We Were, starring Barbra Streisand and Robert Redford.
- Crichton learns from Zhaan that Aeryn is leaving Moya, so he goes to confront Pilot. "Let's hash this out right here, right now.", Crichton announces. "Five cents, the doctor is in." Let's hope he doesn't try yanking away a football before Pilot can kick it.
- Single Tear:
- Temporary Love Interest: Played with. Crichton almost seem envious, despite Velorek being dead. But then, Velorek got to experience a side of Aeryn that Crichton didn't know existed.
- Villainous Demotivator:
- Crais isn't happy with the slow pace of his project. When Velorek lists off a myriad of excuses for the delay, Crais advises him to "take a lesson from your new Pilot: Anyone can be replaced."
- Pilot struggles in his bonds as he's lowered into his new home — Moya. Velorek gently reminds him of what they discussed and encourages him not to be afraid. Crais storms in, looking like he needs a vacation, and Velorek immediately drops the "buddy-buddy" stuff and tasers the heck out of Pilot.
- Wait Here
- You Sound Familiar: Melissa Jaffer provides the first Pilot's voice, after playing the aged Nilaam only a few eps before.
- Your Approval Fills Me with Shame: As Velorek is being led away, he turns to Aeryn and remarks that he always knew she was "special." Aeryn, exalted and damned in one breath, can only stare ahead in self-disgust.