The genius of “Through the Looking Glass” is that it manages to take what is actually a pretty straightforward concept, both literally and metaphorically, and to make it high-concept through execution. At the beginning, all of Moya’s passengers, including the newcomer, Chiana, are sitting together, having a meal in the kitchen, a very domestic sort of situation except that instead of the heartwarming scene we might expect when everyone unites for a meal on another show, they are actually having a serious discussion about whether they should abandon Moya. Her issues with starburst have further worsened as her pregnancy has gone along, and they are all faced with the potential danger of not being able to escape enemies should they arise. Interestingly, though, one can certainly see that they have all grown since the first episode, as none act callously or simply in their own self-interest. For one, they are having a conversation about the issue rather than all splitting off without a moment’s notice and with no feelings of obligation to one another. Furthermore, the interesting thing is that John, the one mainly arguing they should stay, is the one who actually has most to gain by remaining there, given that his way home likely lies in the Uncharted Territories (as he says, it’s “where the wormholes are”), and so if anyone is being selfish on any level, he is, in wanting his friends to stay there with him. But he fully admits this and even understands where the others are coming from.
What sets the plot in motion is when they realize that Moya, through the DRDs, has heard everything that they’ve been saying, and consequently, so has Pilot. And they are both very saddened by the idea that they would want to leave. Now, this is actually very interesting, because it’s the first time that we’ve ever seen Moya actively spying–for lack of a better word–on her crew and expressing her feelings so directly through Pilot. In earlier episodes, the people aboard Moya were basically compared to the equivalent of microbes living in her of which she was mostly unaware–not meaning that she didn’t know they were there but in the sense that they existed on such a different plane of existence that for all intents and purposes she sensed their presence more than she thought of them as friends to communicate with. She didn’t even seem to be as forthcoming with Pilot, who she instinctively turned on in order to protect her baby in “They’ve Got a Secret”. I don’t believe this an inconsistency, however, but rather a reflection of how far they’ve all come as a family since the beginning.
For years, Moya was a prison transport ship, herself a prisoner of the Peacekeepers. It makes sense that, during such a horrific time in her life that she would have emotionally distanced herself as much as she could from her crew. Even further, the Pilot we know and love today isn’t her first Pilot and was forcibly rather than naturally bonded to her after the PKs murdered the original one (as we learn in next season’s crucial “The Way We Weren’t”). After the escape, much of the ex-prisoners’ behavior she did ever happen to take note of involved them being at each other’s throats and at one point even inflicting violence upon Pilot in their own self-interest. No wonder she didn’t trust any of them. However, this all changed with “They’ve Got a Secret” when John spoke to her through a DRD, addressing her directly, treating her as the fully sentient being that she is, and expressing the love that he and all of the rest of them, including Pilot, have for her and her baby. That is when the trust really began and when Moya opened up and started emotionally connecting more with Pilot and the others, the exact moment that all of the people aboard her started to feel like a cohesive unit for the first time. And on repeated occasions since that time, she saw them standing up and protecting both her and her baby, most notably in “Durka Returns,” making her feel even more loving towards them, and Pilot, as well, their relationship growing even more symbiotic and she transmitting her emotions to him even more directly than before.
And whereas in “They’ve Got a Secret,” Moya caused trouble for the crew, nearly costing them their lives while trying to protect her unborn child, here she causes trouble for the crew while trying to prove herself to them. She’s so worried about the prospect of them leaving due to her current perceived deficiencies that she attempts to starburst for them, even though she’s not ready and doesn’t have enough propulsion to get them out, in the process getting stuck in starburst and splitting off into four parallel dimensions based on the color spectrum, into which the characters are divided: Crichton, Zhaan, Chiana, and Pilot in the “regular” Moya, D’Argo in the “red” Moya, whose light is so intense, it causes dizziness and nausea, Aeryn in the “blue” Moya, in which overwhelming, screeching noise is constantly blaring to the point that you can’t hear yourself think, and Rygel in the yellow dimension, which basically has the effect of making anyone within it deliriously high. John soon finds his way from one dimension to the next, gradually figuring out what’s happened and, finally, after speaking to an advanced interdimensional alien that seems to exist between realms and who at first seems to be attacking the ship but actually only wants to set it right (and interestingly, John is the only one who doesn’t want to immediately fight it, proving that he’s learned his lesson from killing the Drax in “Exodus from Genesis”), executes the plan to get everyone to safety. In order to do this, he has to go from dimension to dimension twice more, giving instructions to his friends in each one of the complex control maneuvers they’ll have to coordinate in Pilot’s den in order to give the ship enough thrust to plow forwards out of starburst, and ending with them all finally winding up together, in the same spot at the same time, laughing and joyfully celebrating their victory together.