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At the beginning of the episode, we see in inmate in an insane asylum (named CJ) escape while the breeding cult is holding some kind of festive ritual next door. CJ seems to have some knowledge of the cult, and sneaks in temporarily, steals one of the snakes, and leaves.
Back in Terminal City, we see that the "freaks'" headquarters has also become a coordination point between the freaks and the other transgenics as they try to keep their siblings from being captured by the police or White's men. Apparently the freaks have toned down their anti-outsider feelings toward other transgenics, as they work happily with Max and Alec, and even Logan. Max and Alec happily go on missions to snatch any transgenics in danger right out of White's hands, as they do now.
Back at Jam Pony, Normal is still crusading against transgenics, but Alec has used his friendship with Normal to persuade him to employ several new people, who are actually transgenics. Logan has taken up residence in Joshua's old house, and has some modest electronic equipment, but still nowhere near what he'd need to start up Eyes Only again. Max and Alec agree to search through the Terminal City buildings for computer equipment that might help him. Max and Alec search through a building that used to have some kind of biotechnology company (before the pulse). They find some promising equipment, and while searching they offhandedly discuss Manticore and Sandeman.
Max finally tells Alec that she lied to Logan about them (Max and Alec) having a relationship to push Logan away. Alec determines to take the computer equipment to Logan and set the story straight. However, Logan will hardly let him say a word, and instead says he just wants Max to be happy, she should probably be with "her own kind" right now, and Alec had better treat her right. Meanwhile, Max has started manifesting weird writing, like tattoos, on her skin. A video conference with Logan leads them to think that Sandeman planned for the runes to develop, and Logan thinks they might be in ancient Minoan.
While the transgenics are circling the wagons, White is busy preparing a new weapon in his assault: his men have discovered that X-5 transgenics have a slightly higher body temperature than normal humans, and so a sufficiently precise infrared detector can pick them right out of a crowd. (I have to applaud this approach, because it is simple, clever, effective, and plausible.) Alec's Jam Pony friend and transgenic Biggs, happens to be the first target of White's men. However, Biggs realizes they are on to him and slips away. What he doesn't realize is that the abortive capture made a news story, and his face is now on the news.
CJ has been hiding in the old biotechnology building, and overhears some of Max and Alec's earlier conversation. He goes to headquarters, and then announces that he's an X-5 transgenic, too. He does some silly martial arts moves, but is clearly not playing with a full deck; no one believes his story, but before they can decide what to do about him, there's a breaking news story: they find out that Biggs was almost captured, and now he's wanted. Alec immediately calls Biggs via cell phone to get him to a safe place, but Biggs has been recognized by a local neighborhood watch group. They attack Biggs en masse, and the next thing we learn, on the news, Biggs has been burned to death.
White's men arrived too late to take Biggs into custody (I'm sure they were SO upset about that), but they did acquire Biggs's effects, including a Jam Pony badge. They storm into Jam Pony, give Normal the third degree, and then make off with Normal's employee files. Original Cindy managed to sneak into Normal's office and swipe Max and Alec's files (and the other transgenics', too?) just in the nick of time; Sketchy sees her and sees Max's names on the files and demands to know what's going on. Later, Cindy and Sketchy talk at Crash, and Cindy gives Sketchy a bit of Max's and Manticore's histories. She tries to convince Sketchy that Max has been a good friend to him, and it doesn't matter if she's a transgenic. Sketchy finally says he agrees, but I'm dubious of his affirmation.
Max decides to track down CJ, who has disappeared again, because she thinks he might have some connection to the breeding cult or Sandeman. She finds him in the old biotech building. As they talk, we quickly realize there's a lot more to CJ's story than had been evident. Sandeman is his father; Sandeman had originally been part of the breeding cult, but when CJ was born, Sandeman realized he would never survive the worthiness ritual (as seen in "Exposure"), and he didn't want his son to die, so he quit the cult. (One has to think it wasn't quite that simple!) Sandeman then started the biological and genetic research that would eventually lead to the Manticore project, and this laboratory was his. Max wheedles CJ into setting up a meeting between herself and Sandeman.
Then, in a brainless move, she goes to the meeting by herself (with CJ). What about letting anyone else have some clue what she's up to or the crucial information she just discovered? Nah. So she goes to the meeting and White shows up - CJ had set her up, because he and White are brothers. I hadn't seen this coming, but it does make some sense with what has happened so far with CJ. White quickly takes Max into custody and ties her up in some kind of warehouse where he's holding a few other transgenics before shipping them out.
White examines Max's new runes, and tells CJ that they are the work of Sandeman. It seems that he can read them, and he claims that they just spout Sandeman's goody-goody anti-breeding-cult "propaganda" that the meek will inherit the Earth. Is his interpretation believable? Or is he just telling CJ a story? At any rate, White figures he'll end Sandeman's effort against the breeding cult right here by killing Max; he's only waiting in order to make Max tell him where his son is. Max refuses, and White begins torturing her.
CJ realizes that Max is the special one that Sandeman used to talk about, so he decides that Max should not be killed. He knocks White unconscious and frees Max. Max immediately runs to steal the truck the other transgenics are about to be taken away in; she waits for CJ to go with her, but White shoots him, so she leaves. (We see later on that CJ is still alive, and back in the insane asylum, with White scolding him.) She takes the transgenics back to Terminal City... the end.
There's a lot going on in this episode. First, we finally get some explanation of how Sandeman, Manticore, and the breeding cult are connected. Apparently Sandeman's desire to save CJ's live turned into a philosophical disagreement with the goals of the breeding cult, so he decided to achieve technologically what the cult had done through selective breeding. Why would he want to essentially copy the results of the breeding cult? Perhaps he knows that a future goal of the cult is to take over society and get rid of "normal" humans, and so he wanted to create a counter-force. We don't really know. He obviously was a real genetics genius to have created Max with her "perfect" DNA and to apparently include "extras", like her new runes. We also don't know how Sandeman's efforts turned into Manticore, although we can imagine that the offer of government funding for his project could have convinced him to work for the government. Presumably another disagreement between him and the government precipitated his leaving Manticore when Max was young. I can admire him for leaving the cult to save his son, but it's not so admirable for him to have abandoned the Manticore children to the devices of their sadistic teachers.
I noticed that neither White nor CJ made any affirmative or negative comment about Sandeman still being alive. CJ didn't say either way when setting up the "meeting", and White just said that he changed his name to essentially disown Sandeman. This is obviously leaving open an opportunity for Sandeman to come into the picture in the future; sadly, the cancellation of the series leaves this thread unresolved.
The assault and murder of Biggs really raises the stakes in the situation in Seattle. The authorities say they don't approve of vigilantes attacking transgenics, but one gets the feeling they don't mind too much. How many transgenics will be killed by the mobs? How many innocent people? In an interesting scene, Alec and Joshua go find the leader of the group the killed Biggs and beat him up. I was surprised that Alec stopped the beating before they killed him - given his and Joshua's high emotion (especially Joshua after Annie), I would've thought the guy was dead. Instead, Alec tells him to get out of town. Unfortunately, this kind of restraint on the part of the transgenics is unlikely to be noticed.
Closer to home for Max and the others, their safe haven at Jam Pony is probably gone. Even if Cindy got everyone's files out in time, one would guess that White's men will be watching the place. Plus, Sketchy knows the truth - how long will he be able to keep it to himself? Does he really think that Max and Alec are no threat?
Fortunately, Max, Alec, and the others are quickly building a new life and home in Terminal City. I can see this situation and the new transgenic characters being put into place to take the series in a new direction for the next season, if there had been one. The show's cancellation makes some of these last episodes even more depressing than they might have been otherwise.
Finally, the situation between Max and Logan has not improved. Whenever they talk, the pain between them is palpable. What will or could happen between them in the series' final episode?