(And we'll get into Lacy eventually, but I think her journey -- understanding and empowering herself as part of the violent, nasty real world -- might be the hardest of all, if only because it doesn't come with magic powers.)
So on a fundamentally gross but all-too-realistic level, you have the grim story of all parents and all children, staring at each other through these murky windows and trying desperately to understand each other, bodies and all. But you also have the fundamental story of men and women -- the story BSG eventually straight-up told -- which is that men have no compelling reason to see women as anything other than very complicated, very confusing machines. But in order for any of us to survive, and I mean our very existence is contingent on this fact, everybody has to make the jump past that red line.
Sam comes walking into Joe's house, since when he knocks nobody answers, and finds his brother IRL for once, looking at old things and being maudlin because Emmanuelle yelled at him. He can barely focus when Sam walks in. One of the things is a cute little art-card, on which Tamara signed her name the way she always did: With a bright flower blooming from the top of the "T." Sam rips it out of his hands, reminding Yusif about the funeral: "You gave the ferryman the coins, you sent her on her way. Shannon, too."
Joe follows his own crazy line of logic to abruptly asking Sam what it feels like to kill someone. If he wants to earn his Tauron stones, he must figure out this particular mystery: How he can shoot someone, even in the Matrix, without losing his nerve. Of course, Sam doesn't know about his drug habit or his trips to the Underworld, so he's just totally offended. Which, it's offensive. He realizes eventually how low Joe's gone, and says they're fine on the botched Amanda assassination, but after some awkward silence and serious puppy-dogs from his brother, he thinks maybe Joe needs to know this stuff after all. Death consumes Yusif, haunts him. But Sam walks with Her. So no matter why his brother is freaking out, Sam can help.
"Tell yourself it's not real. And then they're not people shooting at you anymore, they're targets. And the whole thing becomes just a game." Which any cube would already know, of course, but is also the terrible line we have to walk, and which most importantly is exactly the wavy blurry line that terrified Zoë so much she changed the world. It stopped being real and started being a game, so she gave birth to a daughter, from her own forehead, who could end it all.