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In a flashback, we learn how Khlyen first came across the green plasma back on Arkyn way back when, how he grew a tree in its glowing soil, and how he told his daughter Aneela to always remember its exceptional qualities. But that was then, and this is now. Pawter is dead, and Delle Seyah is running Old Town into the ground.
Onboard Lucy, Johnny is struggling to come to terms with the death of the woman he loved. And Fancy Lee is struggling to come to terms with D'avin's arm, which is squeezing the life out of his neck. Three Black Root agents arrive looking for Khlyen, who reveals himself and shoots the sixes with a serum that makes them vomit up their green goop. Khlyen whipped up the recipe after studying D'avin so closely, and if they can infect the plasma with it, they can save the Quad. Brilliant. Unfortunately, the team can't destroy the stuff on Arkyn because the place is crowded with Sixes. But if they can find the parent source of the plasma, in the form of that same tree Khlyen planted; they can kill the tree and it will have ripple effects that will disrupt the green stuff's power and scope. And that tree is sitting in a potter in a high-security, elite depository called Archive in the Chrome Nebula. Dutch will need to pull out her fanciest clothes and snootiest attitude to get them access. In transit to Archive, Khlyen calls up Delle Seyah and informs her of the Killjoys' plans, and requests a meet-up back in Old Town upon his return. That two-timing son of a…!
D'avin and Fancy Lee take care of the first team of security guards, while Dutch and Khlyen sweet talk glorified bank teller Serafin, and then defeat his round of guards. Meanwhile, while everyone else is taking their sweet time, Johnny is trying to evade two falcon ships hot on his tail. Once they get past the defenses, Dutch and Khlyen get face to face with the source of the plasma — the tree — and dump the poison in it. But it doesn't take: the poison needs to bond with human tissue to speed up the process. But where are Dutch and Khlyen going to find a…oh, Khlyen sacrifices himself. Khlyen, the man Dutch has hated so much for so long, now dies in her arms. And she's feeling the feels. The pond under the tree turns black, and the green rivers on Arkyn do the same, and all the Arkyn plasma in the Sixes is rendered inert.
Dutch, D'avin and Johnny toast their bittersweet victory at the Royale, but Johnny is soon overcome with the sad remembrance of his dead Pawter and must step out of the bar. Who does he happen to cross paths with but Delle Seyah, who is under the impression that she's supposed to rendezvous with Khlyen. Ah, so it was Johnny who impersonated Khlyen to the murderess in chief — very sneaky Johnny. Well, their meeting is cut short when Johnny shoots Delle Seyah in the gut and leaves her to die in an alley in Old Town. Like the rat she is.
Now a fugitive, Johnny must skip town lickity split. But Lucy won't let him go without a proper goodbye. She also won't allow him to cavort through the galaxy without a companion, and so she calls in Clara to be his traveling partner (remember her? The half cyborg from the season opener?). And back at the Royale, Dutch and D'avin are surprised by Fancy Lee, who's just a plain old human now thanks to the plasma in him expiring. Down a Johnny but up a Lee, Dutch is ready to take on Aneela wherever she may go, whatever havoc she may wreak, whenever she may wreak it. It's on!