It's time for a recap. Ron Moore's Battlestar Galactica returns to us this month having sparked in the third quarter of last year some fairly passionate debate. It is a sign of the show's quality that it can encourage such comment, but at the same time much of the discussion revolved around a profound and increasing sense of discomfort with the show's content, in particular its treatment of the Cylons and, by extension, gender.

I reviewed the first four episodes of Galactica's second season in September, and pointed out that there were questions to be asked concerning the show's penchant for depicting the seduction of dimly good-intentioned human males by malevolent seductress robots. I gave the episodes the benefit of the doubt. The instalment which immediately followed that opening quartet, 'The Farm,' rather put paid to my wait-and-see policy: Kara 'Starbuck' Thrace, the swaggering, talented female starfighter pilot, is kidnapped by the Cylons and informed by a male doctor posing as human that her reproductive system is her "most valuable asset these days." Starbuck has little interest in children or procreation, insisting that she "is not a commodity."

When Starbuck contrives her escape from the compound, however, she stumbles on a breeding farm, in which unwilling women are integrated into machines and used as biological incubators. She destroys the farm—killing the raped women in the process—and flees back to the lines. The question that has lurked in the background of Galactica's run so far rears its ugly head: if the human men, Balthar or Tyrel or Agathon, get to mate with beautiful women, why is it necessary for the human women to be plugged into machines, dehumanised and objectified?

The final episode of the run, a cliffhanger designed to leave us panting for 2006, saw Galactica come across another surviving Battlestar of the human fleet, the Pegasus. Commanded by the distant and formal Admiral Helena Cain, we discover that the crew of the Pegasus have interrogated their Cylon captive—a version of Balthar's ex-lover and constant invisible companion, Tricia Helfer's sensual and sinister Number Six—by means of abuse, torture, and rape. They soon attempt to extend this treatment to Galactica's own Cylon prisoner, a version of the Raptor pilot, Sharon 'Boomer' Valerii.

These scenes are unflinchingly graphic. When Balthar first encounters the catatonic prisoner onboard the Pegasus, we can immediately guess what has been done to her (though the slow reveal of the full truth is one of the few instances of our feeling fully at home and empathetic in Balthar's increasingly unstable shoes). In some ways this is disappointing: Battlestar Galactica regularly flouts conventions and audience expectations, and it seems a shame for it to fall back on stock images and situations in so sensitive a situation. You could suggest that the audience should have instead been shown an abused man, been asked to engage with gender roles rather than merely accept the generally accepted, but to do so, would, I think, miss the point that using a character with whom we are completely familiar was the only choice that could have made dramatic sense of the scene.

Because, as troubling as the gender issues are in these episodes, they do not seem to me the focus either of these five episodes, or of 'Pegasus' in particular. The Number Six stored in Balthar's mind exhorts us to consider the abused woman as an individual, a reality, rather than a scientific problem or icon. Balthar later observes that her catatonic state emphasises more than anything else so far that the psychology of those Cylons who appear human is identical to that of the beings they imitate and destroy. When Cain, assuming command of the fleet, splits up the Galactica's crew on the grounds that Commander Adama is too close to them, and when Apollo is told by his new CO that he should not allow the problems of his friends to trouble him, what is really going on is a destruction of the very philosophy that has kept the understaffed crew of the obsolete Battlestar alive: their acceptance of individuality.

It is in 'The Farm,' that same episode in which women are wired up to egg-extraction machines, that Adama discounts the possibility that Boomer is a machine, and says without doubt that Chief Tyrel was in love with her. Later, in 'Home, Part 2,' Starbuck will observe that Agathon's love for Valerii is real, that it makes no allowance for her origins. In the same episode, Sharon insists that her memories are so strong that she may as well have lived the human life with which she has been programmed—in short, it is the identity bestowed by her memories that makes her who she is. Our individualism is our strength.

And in the first part of the same story, Balthar briefly perceives the crew as a swarming mass, eliciting the comment from Number Six that he is beginning to see them as the Cylons do (those same Cylons, remember, who were capable of exterminating the entire race). For all her saintliness, President Roslin fails to see Boomer as anything more than a representative of the Cylons, having no compunction about jettisoning her from an airlock. Even the enlightened Adama ceases to perceive Boomer as an individual at one point, attacking her and attempting to kill her. When the humanity of empathy is removed—when Starbuck is sent on a mission, and Roslin's telephone calls ignored—the unforgiving military hierarchy takes precedence, and events spiral out of control very quickly. In 'Final Cut,' a journalist makes a documentary about the Galactica crew, at first seeking ways to condemn them as a uniform military bloc, but ultimately concluding that they are men and women, individuals like the rest of us, struggling to do their jobs and get by. 'Pegasus' shows us what happens when the understanding style of command that Adama has constructed is swept aside.

And yet the problems remain: Boomer is saved by her men, for example, who charge to the rescue in a testosterone-fuelled bout of protectiveness. It all happens so fast, spurred by a bullish fight between the alpha males of Pegasus and Galactica, that one can't help but roll one's eyes. At the same time, however, this problem is an extension of the wider one on show in 'Pegasus,' and to an extent all of these episodes: that of pacing. That opening quartet of episodes was intense and unrelenting, but here the pace of events is less perfect. 'Pegasus' is too compacted, too rushed, to the extent that it sometimes feels like the Galactica crew have stepped into the equivalent of Star Trek's mirror universe, so black-and-white is the contrast between them and their Pegasus counterparts (a problem which further compounds the clumsy treatment of the difficult issues addressed in the episode). 'Home, Part 1' seems curiously slack, whilst 'Home, Part 2,' in which the crew discover the whereabouts of Earth and the audience realizes that the 12 colonial gods equate directly to our own Zodiac, fits a great deal into its scant minutes—a curious choice for episodes sharing a plotline. The fourth of these five episodes, 'The Flight of the Phoenix,' is a typical spacer episode of the sort we're not used to in this time-constrained series, featuring the ludicrous propositions of a deck crew constructing a starfighter from scratch and Boomer using a wire thrust into the veins of her wrist to communicate a virus to a Cylon attack fleet. But with the stretching of season two to twice the length of season one, perhaps we must begin to expect a more leisurely, even a more hit-and-miss, style of pacing.

It's not as if these episodes did not set us up for this month's return: Boomer seems to be lying when she suggests she is not wired into a wider Cylon matrix and can't remember her previous incarnations ("and you ask 'why'?" she whispers to Adama after his attempted murder of her, a reference to something he said to the corpse of the previous Boomer); Balthar's relationship with the Number Six in his head is changing, to the extent that he can now banish her at will; and, of course, the Pegasus remains in the mix. There are some who have all but lost faith in the show, believe that it has abandoned its intelligence and refusal to endorse stereotypes. But in truth these episodes continue to push the idea that we are all individuals, that blanket judgements are destructive. These five episodes were confused in execution rather than concept, damaged by pacing not prejudice. It would be a shame not to give the show the chance of proving this by at least watching what is, after all, the second part of a contentious storyline.

So. Are we all up to speed? Good.

Let's hope Battlestar Galactica is, too.

Dan Hartland is a freelance creative thinker figuring out what to think. A writer and musician of the inverted commas variety, he splits his time equally between these two things and procrastination. He comes to science fiction from outside the genre, and is a little too happy to remain a gadfly.