!The Past
Young Ned runs away from BoardingSchool, and happens across a group of kindergardeners on a field trip. They are exitedly eyeing a birds' nest, hoping that the baby birds they imagine are inside will fly away; the baby birds are dead, but Ned, hoping to connect with the other children, resurrects them. Unfortunately, the baby birds are kept alive by the sacrifice of... the baby birds that the children had been raising from hatchlings and were planning on releasing that day. Ned learns that new beginnings are painful.

!The Present
Ned and Chuck now live in separate but adjoining apartments. Chuck revels in her newfound independence--it's the first time she's lived alone--but Ned, though he tries to hide it, is miserable.

Emerson is retained by Georgeann Heaps to find her missing daughter, Nikki. He, Ned, and Chuck trace Nikki Heaps to an RV owned by a mime... one who now lies dead, poisoned by his makeup. The mime explains that Nikki ran away to join the circus, and was last seen in the company of a group of clowns.

At the circus, the trio meets a snooty FrenchJerk acrobat and interrogates the manager, who says he doesn't remember Nikki but who is clearly lying. And it's not just Nikki who's missing--so are ''all'' the clowns.

The clown car (with clowns) turns up in a nearby lake, without Nikki. The detectives wonder just how radical her new beginning was intended to be: is she still essentially the same person, or has she really discarded all the trappings of her past and made a fresh start? The question is also applicable to Emerson's search for his daughter as well as to Ned and Chuck's relationship.

They eventually discover that Nikki and the manager were in cahoots to scuttle the clowns' attempts to unionize.

!Tropes
* AppealToObscurity
-->'''Emerson:''' Have you ''seen'' the special lockup they keep for cocky young acrobats? Because ''I'' haven't.
* BawdySong: A limerick: There was a young man named von Dinas...
* BilingualDialogue: {{Omniglot}} Chuck speaks a line of French to the acrobat.
-->'''Chuck:''' Je peux parler avec Nikki une minute? (Can I speak to Nikki for a minute?)
-->'''Acrobat:''' ''Une'' minute! (''One'' minute!)
* BoardingSchool
* BindleStick: Used by runaway Ned.
* ButterflyOfDeathAndRebirth: In a subtle use of this trope, the kindergarteners wear butterfly wings.
* ButtMonkey: Von Dimas, a volunteer at the circus the night Nikki disappeared. They stripped him to his underwear, had the rest of the audience throw chocolate pies at him, and then gave him a "shower" (it involves a horse named Peppers and lots of chocolate diuretic).
* CurseCutShort
* CymbalBangingMonkey
* EnemyMime: Averted; Chuck ''likes'' mimes, though Emerson doesn't.
* FrenchJerk
* IllNeverTellYouWhatImTellingYou: Chuck slyly gets more information from Nikki's best friend than the friend had planned on revealing.
* ImprobableAimingSkills: Ned, at the circus.
* InnocuouslyImportantEpisode: Some viewers disliked this episode at first, but there is no episode more crucial to setting up the arcs and themes of the second season: the corrosive effect of secrets; something new beginning as necessarily implying something else ending; stasis as the opposite of life/death/rebirth; the impossibility of simply picking up a relationship where it was left off; one's persona or public self versus one's True Self; a parent's inability to recognize his or her child.
* NoIndoorVoice: Von Dimas.
* OverlyLongGag: The clown car scene
* RetroactiveRecognition: Hayley [=McFarland=] as Nikki Heaps, who would go on to become [[Series/LieToMe Emily Lightman]].
* TheRunaway: Ned as a child, Nikki Heaps.
* SoundEffectBleep / NarrativeProfanityFilter: As Ned is telling Emerson what he learned from Miss De Jong, we see flames shoot out in front of them from a flamethrower act; when the flames disappear, Ned has just finished telling his story, and a bemused Emerson responds, "I've never heard ''you'' use ''those'' words before."
* ThereAreTwoKindsOfPeopleInTheWorld