Wracked by high fever, Sarah Manning (Tatiana Maslany) slips into delirium midway through “Certain Agony of the Battlefield” and comes face to face with the origins of Orphan Black. Infected via blood transfusion with the Castor clones’ STD, she passes through a tunnel in her mind’s eye only to greet Beth Childs in a gauzily lit kitchen of the afterlife, where she receives a message from her late “sestra” to the tune of the straining score. “We do terrible things for the people we love,” Beth says, referring to the impenetrable Paul Dierden (Dylan Bruce). “Stop asking, ’Why?’ Start asking, ’Who?’” Thus freighted with delusions, dream sequences, flashbacks, and musical interludes, “Certain Agony of the Battlefield” strings together a series of arresting images, but by the time Paul unwraps a grenade from his palm in the final minutes of the episode, these flickers of style add up to little more than a placeholder for dramas still to come.

Tonight’s episode of Orphan Black, “Transitory Sacrifices of Crisis,” comes all too close to the grievous error of which its title warns. Alone, the phrase, cribbed from Eisenhower’s Farewell Address, may suggest light at the end of the tunnel, but in context it’s the very sacrifices we make on the altar of expediency that set us up for disaster down the line. “To meet it successfully,” Eisenhower says of the Soviet threat, “there is called for, not so much the emotional and transitory sacrifices of crisis, but rather those which enable us to carry forward steadily, surely, and without complaint the burdens of a prolonged and complex struggle.” Suddenly consumed by the need to explain Project Castor, by its crisis of narrative, Orphan Black seems increasingly willing to jettison the rich characterization of the “sestras” in favor of constructing conspiracies, and “Transitory Sacrifices of Crisis” may be the show’s worst episode to date.

“You’re a legend, Sarah Manning.” So one of Project Castor’s menacing clones (Ari Millen), imprisoned by the Dyad Group, pays his respects to the former con artist (Tatiana Maslany) in the season premiere of Orphan Black, as the genetic “sestras” of the series confront yet another amorphous enemy. It’s the subtext of the scene, however, that suggests both the strengths and the weaknesses of tonight’s episode, for the Castor clone’s greeting might also be taken as an acknowledgment of Maslany’s incomparable talents. “The Weight of This Combination” once again offers evidence that hers is the best performance on television, but it remains unclear if Orphan Black can keep pace.

“Men observe when things hit, and not when they miss,” Francis Bacon once wrote, “and commit to memory the one, and forget and pass over the other.” Published posthumously, his “natural history, in ten centuries” Sylva Sylvarum is a pastiche of “experiments” in the philosophy of science, but his aphoristic caution aptly describes the dangers of the episodic review. Weighing the merits of individual installments in a beloved series, particularly one as disposed to bouts of whiplash as Orphan Black, the standout moments tend to linger while the disappointments fade. The second season finale, however, provides an opportunity to reconsider the whole. “By Means Which Have Never Yet Been Tried” is best understood as a microcosm of the previous nine episodes: plagued by the same intractable flaws and buoyed by flashes of brilliance, a sloppily written marvel of editing and performance.

If you follow these weekly recaps of BBC America’s almost-great drama with any regularity, you know by now that I take Orphan Black’s allusions to the prolific work of English philosopher and scientist Francis Bacon seriously. It may simply be a writer’s prejudicial affection for the clever arrangement of words, but in truth such signposts crystallize both the thematic thrust of the series as a whole and the strengths and weaknesses of each individual episode. Bacon’s complex alchemy of faith and reason is the framework in which Orphan Black situates its suspicion of any system or institution that threatens to elide the personal and the familial. His words frequently reflect the stylistic and narrative messiness (“Governed As It Were by Chance”) or precision (“Ipsa Scientia Potestas Est”) of individual episodes, as though a self-reflexive comment on the episode’s shape. In this vein, “Things Which Have Never Yet Been Done” perfectly describes the penultimate entry in Orphan Black’s often inspired, sometimes vexing sophomore season: Pushing the series into previously unexplored terrain, the episode counts among the best hours of television I’ve seen so far this year.

In “Variable and Full of Perturbation,” Ethan Duncan (Andrew Gilles) reads to Kira (Skyler Wexler) from The Island of Dr. Moreau, H.G. Wells’s 1896 novel about a mad scientist experimenting with the creation of human/animal hybrids. “How does it go?” he asks Rachel (Tatiana Maslany) later, revealing that they read it together in bygone days. “The bit about how he’d be forgiven for hate, but not for irresponsibility?” The allusion to Dr. Moreau is a fitting complement to the Dyad Institute (after all, both interfere with human individuality in the name of some abstract, directionless “science”), but “Variable” is jumbled and strange. Two episodes from season’s end, Orphan Black appears no closer to revealing the puzzle’s final shape.

The most inexplicable and, well, delightful twist in “Variable” is the appearance of Tony, the Clone Club’s first trans man, played by Maslany with the Canadian-accented coarseness of a transient rough. Tony’s long, tangled hair and unfortunate beard belie a loyal, if somewhat randy, soul. It may be a measure of how much Orphan Black has won me over, warts and all, that watching Tony sidle up to Felix (Jordan Gavaris) for a kiss left me so discomfited. A protective pang sounded in my head when I realized that Felix sleeping with his foster sister’s lookalike was bound to end badly. In fact, the sweetest moment involving Tony comes when he’s off screen, as Orphan Black sneaks in a little instruction on the appropriate pronouns. “So, I got it right,” Art says. “She’s a trans clone.” “He’s trans,” Felix replies. “He’s, yeah.”

Family Day at the New Path Wellness Center features neat rows of pastel-colored name tags and, as Felix (Jordan Gavaris) observes, “some kind of public flagellation,” a felicitous setting for the crazed brilliance of “Knowledge of Causes, and Secret Motion of Things.” The frustratingly inconsistent second season of Orphan Black has been a tale of two series, zigzagging from merely serviceable to wholly magnificent, and “Knowledge of Causes” qualifies as the best of times. Focused, witty, and energetic where “To Hound Nature in Her Wanderings” was distracted, self-serious, and flat, this episode is a giddy reminder of the show’s intermittent greatness.

“Dyad’s a hydra,” Mrs. S (Maria Doyle Kennedy) says in the closing minutes of “To Hound Nature in Her Wanderings,” referring to the Institute’s secretive, multipronged structure. The poisonous, many-headed serpent of Greek mythology is a similarly useful metaphor for the episode, which seems to sprout two new twists for each one it threatens to resolve. The episode is either a hideous plot dump or a heady brew of unexpected juxtapositions, and sometimes both at once, forging strange new alliances from the fragments of the season’s first half: between Helena (Tatiana Maslany) and Grace (Zoe De Grand’Maison), Mrs. S and Paul (Dylan Bruce), Art (Kevin Hanchard) and Felix (Jordan Gavaris), Angie (Inga Cadranel) and Vic (Michael Mando).

Tough love hurts. In “Ipsa Scientia Potestas Est,” a rollicking mid-season wallop that counts among Orphan Black’s best episodes, the cruelty of kindness justifies cuffing hands, sewing shut lips, and stripping bare, though in the end a gentler approach proves more effective. “Knowledge itself is power,” the Latin of the title promises, but when it comes to understanding people, delicacy is often better than force.

“The spirit of man,” Francis Bacon wrote, “is in fact a thing variable and full of perturbation, and governed as it were by chance.” Narrative perturbations abound in the latest episode of Orphan Black, breaking the stalemates of Project LEDA, Helena’s captivity, and Alison’s substance abuse as the sophomore season launches into its second act. But even as it disrupts the geometry of the central clone quartet, the grimly utilitarian “Governed As It Were by Chance” encapsulates certain of the show’s weaknesses as surely as “Governed by Sound Reason and True Religion” testified to its strengths.