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A number of different plots intertwine in this episode, so I'll hit them in an arbitrary order until they cross. Joshua is still broken-hearted over the death of Annie and can no longer stay in hiding in Sandeman's house. He decides to go to Terminal City (previously visited by Max and Alec in "Proof of Purchase"), where many of the non-human-appearing transgenics are allegedly living. Terminal City is contaminated by toxic waste, but the transgenics are able to survive there.
White tracks down a transgenic he believes is Max, but it turns out to be her clone, Sam, who has the next higher designation. (This is nicely precedented with the "twins" Ben and Alec.) Sam was on a deep-cover mission when Manticore was destroyed, so she continued with her cover and fell in love with her "husband" and "son", who don't know who she is. White now has them in custody, but tells Sam that he'll let them go if she brings him Max. Sam is already angry with Max for breaking out of Manticore 10 years ago, thereby subjecting Sam (and the other clones, like Alec) to intensive scrutiny at Manticore, lest they also decide to escape. Sam quickly starts tracking down Max, and we see that she has a very different personality and is not averse to using guns.
On the news, the media is flaming the panic over the "mutants" to a frenzy. Congress is holding hearings on the transgenics and Manticore and how this situation occurred. White is called to testify, and his government boss tells him to plead the Fifth Amendment. White's breeding cult superiors have other plans, however.
At Jam Pony, Normal and some of the employees are getting pretty paranoid. In a shocking move, Normal pulls a gun on someone he thinks is a transgenic after a practical joke. Max zips by and grabs the gun from him, defusing the immediate situation, but causing a lot of suspicion about her. Alec warns her later to avoid Jam Pony because of the paranoia there.
As Sam begins tracking down Max, she incidentally encounters Logan. The first time, she ignores him, since she doesn't know him. When he comes by Jam Pony while she's checking it out, she quickly blows him off and picks up enough clues from Logan to tell him it's over. Logan is upset, but I also get the feeling he knows something's a little off about "Max".
Max feels like she's finally hit rock bottom in her life: she's broken up with Logan, Joshua is abandoning her for Terminal City, the transgenics are feared and hunted, and she personally is under suspicion at Jam Pony. She decides that it's time for her to leave Seattle (wouldn't Zack be proud!). Original Cindy tries to convince her to stay, but she's determined. As she leaves the border gate of Seattle on her motorcycle, Sam finally catches up with her on her own motorcycle.
Meanwhile, White's men have finally traced one of Logan's Eyes Only hacks. Logan knows that he has been located, but he manages to remove and/or erase crucial information on his computers before he abandons his apartment. White's men arrive and shoot up Logan's apartment; White himself arrives and smirks about Logan's whiteboard diagramming the connection between the breeding cult and Manticore. Logan is leaving the city when he sees what appears to be two Maxes in succession zipping by him. He's no dummy, and realizes something is up.
Outside the city, Sam shoots out one of Max's motorcycle tires and then ties Max up in an abandoned industrial area while Max is unconscious from the accident, then calls White. When Max comes to, Sam more or less explains her situation, but she doesn't even consider trying to work with Max to get her family back. She has nothing but score for Max for running from Manticore, especially since it looks like Max is running from her problems now, too. Strangely, Max does not try to convince Sam that White will renege on his deal, try to explain what White is, or tell her how she worked against Manticore. I can only think, that this is because of her general depression.
Logan tracks them down and almost gets the drop on Sam, but at the last minute is unsure which one is Max and which is Sam. Sam knocks him out, but is distract enough that Max can escape her bindings. Max and Sam begin some hand-to-hand fighting, and Max manages to knock Sam out. With Sam under control, Max and Logan brainstorm about what to do - Max is not about to let White keep Sam's family. When White shows up, Max poses as Sam and distracts White long enough for Logan to conk him over the head.
Joshua has finally arrived in Terminal City and makes contact with his "brothers". They have a whole defense organization, for defense against "ordinaries" as well as rival transgenic organizations, such as the one most X-5s are in. Alec tracks down Joshua to Terminal City and is temporarily allowed in as a friend of Joshua.
Max contacts White's men and arranges a trade: White for Sam's family. She demands that the trade happen in Terminal City. Although White's men don't know it, this is the ace in the hole for her: she knows the transgenics there will be watching, and she's gambling on Joshua knowing what to do. (Alec being there is an extra bonus.) The trade begins, but sure enough, White has a hidden gun, and so he tries to capture Max, Sam and family, and Logan. But Joshua and Alec have the local transgenics surround them with numerous weapons. White sees reason and lowers his weapon. Frankly, I don't know why the transgenics don't take White hostage (at least) right then and there - I can't believe Joshua let White go after Annie's murder. Maybe he didn't figure out White did it. Anyway, I guess Max wants to keep her word on the deal.
White and his men leave. Max, Sam and family, and Logan get to meet Joshua's new friends. Logan arranges for Sam and her family to escape to lovely Canada. Max decides that she isn't going to leave Seattle after all. She makes some overtures to Logan, and she returns to Jam Pony in defiance of their paranoia.
We see White testifying before Congress and revealing everything, much to the ire of his government boss. He plays up the danger of the transgenics to the public. We find out that one of the senators on the committee is a member of the breeding cult and promises to take care of White.
There's a lot going on in this episode. Despite the whole Max-has-a-clone thing, I thought the most significant event was the change in Joshua. Annie's murder has uncovered Joshua's harder side, and we can certainly understand why he would want to be around others of his own kind. His turning his back on the world was nicely symbolized by him painting the windows of his house black. Max was unusually desperate to control his actions and not let him go to Terminal City - she herself was feeling loss and didn't want to lose him, too. Uncharacteristically, Joshua pushed back against her and basically told her to get lost. What's going to happen with Joshua and his new friends? They don't seem too eager to be friendly with Max and Alec, since they are X-5s, but will Max try to unite the transgenic groups?
Another major change is the end of Eyes Only, at least for awhile. Logan will need a lot of money to get new equipment and a new safe location before he can get his operation going again. Will he try to do so, or will he find a new mission in life? In some nice continuity, Logan's blood transfusion from Joshua in "Hello, Goodbye") has returned some movement to his legs, as his transfusion from Max did in the first season. Is this another false hope?
Sam was an OK addition to the show - I didn't find her personality that interesting, I guess. While we could sympathize with her situation, since she just kept harping on Max, it didn't make me like her much. I found her rather naive that she didn't even think about how she was going to ensure that White kept his end of their deal or maybe try to work with Max. I guess she doesn't have the "family values" that Zack instilled into Max and the rest of their unit at Manticore. Introducing Sam as a daydream of Max's was an interesting device, although a little confusing at first.