All things considered, the revelation of another cloning experiment that produced male clones is something Orphan Black has had in its back pocket all along.

Whether the twist changes things for better or for worse remains to be seen. Tatiana Maslany’s performance(s) are the core of this show and, no matter what, it will always be at its best when it focuses itself around the characters she plays. Orphan Black just gets better when it puts some of the clones in a room together, and in this finale they finally get four members of the Clone Club (yes, including Helena) to spend some quality time together (clone dance party!).

There’s rougher material before and after the brilliant scene where Sarah, Cosima, Alison, Helena, Kira and Felix have a sleepover, but this episode largely works by asking just as many questions as it answers and making us eager to see where things go next.

Rather a lot happens, and all the plans, double-crosses and conspiracies interweave a little much and make things confusing. At one point Cal reappears and soon afterwards says, “OK, so what’s happening now?” It’s almost like he’s echoing concerns viewers surely have about this rushed and muddled end to the season.

Everything erupts in the immediate aftermath of Kira’s kidnapping, sending Sarah to take the most unlikely action by handing herself over to Dyad. All of a sudden, though, it seems like everybody else has mobilised to help her out.

Taking Kira is a step too far, it would seem, so Duncan offs himself (his perfect dying words to his daughter – “You don’t deserve me anymore…”) to cut off Rachel’s supply of his scientific knowledge, Cosima gets working (with the help of Scott) on a fairly ludicrous way to help Sarah out, while Cal and Mrs S both take advantage of the double agents they have within Dyad and the military.

This episode does answer a lot by telling us where Paul fits into the whole thing and bringing Cal into proceedings in a believable way. Its best scenes are the simplest ones, like the aforementioned clone dance party, or Sarah’s conversation with Cosima where she worries about how she’ll continue to face the forces of Dyad without her sister.

Helena gets most of the emotional material, as her meeting her sisters is as wonderful as expected. There’s a really unnerving edge to Sarah’s ordeal too, as we get a glimpse into just how terribly Dyad treats people that it considers to be property.

In the end, not every element of this finale works as smoothly as it could. Cosima’s pencil-firing weapon turns out to be useful but is rather elaborate in its construction and doesn’t get rid of Rachel so much as give her a more villainous appearance for whenever we next see her. Cosima seems like she’s about to die, but then discovers Duncan’s potentially life-saving research. She and Delphine have been separated, though, and it doesn’t look they’ll be getting back together so easily.

A surprising twist near the end reveals that Helena’s being used as a bargaining chip by Mrs S. We have no idea what the military want with her, but we do now know they are responsible for a cloning operation of their own.

It’s one of Orphan Black’s most substantial developments so far, as we see that Ari Millen’s Mark (a Prolethean with a military-backstory who has been on the sidelines for most of the season, save for his relationship with Grace) is just one of many to share the same face. This is Project Castor, the military’s equivalent to Project Leda.

There’s a lot that happens here, with big questions about the conspiracy answered and some answers – like exactly who Marian Bowles is – taking the show in new, exciting directions (it just has to get another season after that ending!).

‘By Means Which Have Never Yet Been Tried’ is largely a satisfying episode with a superb twist that makes for a strong finale to the excellent second season of Orphan Black.

Aired at 10pm on Wednesday 2 July 2014 on BBC Three.