Previously on Fringe, Olivia told Silver Nina they need her help, which Silver Nina seemed more than happy to provide; Michael the Junior Observer met the Fringe team in the alternate timeline; the current Fringe team tracked him down via the radio signal. Well, that wasn't so much – how complicated could this episode be?

After Peter is able to ascertain that Michael doesn't have an implant in his neck, which may or may not be important later, the Fringe team tries to get Michael to tell them about Walter's lost plan with Donald; when Michael stays silent, Walter wants to put him on a coma and pump him full of drugs, and Olivia is like, "Ixnay," but she does wonder why Michael no longer exhibits his empathic abilities, so she calls Nina for help. Unfortunately, thanks to the Fringe team's recent use of the sublimation device, Windmark and the Observers know that someone in the Ministry of Science has betrayed them, and their money's on Nina, a suspicion they confirm in some kind of C.S.I.: Observers sweep of her office. Nina meets with the team and tells them some equipment she has in a "black" (i.e. off the Observers' grid, somehow) lab may be helpful in communicating with the boy; Peter also takes the opportunity to express his displeasure at Nina's promise to remove the pieces of Walter's brain once the world is saved, to which Nina points out that if the plan isn't completed quickly, Walter may regress completely and no longer want to go through with the procedure. She adds that anything worth fighting for comes with a cost, which is a total throwaway line that will have nothing to do with anything.

Nina takes the crew to the black lab, wherein they see, from the handful of apparently-dead Observers around the place in pods, that the Resistance experimented on Observers to try to find ways to fight them, but their scientists weren't able to extract any useful data. However, Nina theorizes the technology they used in their attempts might be useful in communicating with Michael; they try it, but when it fails, Nina realizes that instead of reading Michael's mind, they need him to try to read theirs, which will require different equipment, which her ally at the Ministry "Hastings" will provide. Unfortunately, this same Hastings is getting mind-probed by Windmark at the moment, and since Hastings has a worse poker face than Homer Simpson, all is soon revealed. The Fringe team breaks into the Ministry anyway and steals the equipment they need just in time to get a bird's-eye view of Hastings being tortured, news that Olivia relays to Nina. The Observers leave Hastings alive for the Fringe team to rescue, and he despairingly tells them that they know where Nina is.

When Nina gets the warning that her time is coming, she goes back underground to the lab, and, presumably moved by the need to say goodbye to someone, tells Michael everything's going to be okay. Perhaps through the force of her feelings, he finally steps forward and touches her face, which seems to impart some knowledge to her. Unfortunately, we don't get to find out what it is – yet -- as the Observers show up (in… a car?) in pursuit. Nina urgently tells Michael to come with her…and when Windmark gets into the lab, he finds only Nina, who, triumphant and unbowed, tells him the fugitives are long gone, and when Windmark sees the evidence of what the Resistance did to the Observers, he expresses cold fury in a way I don't think we've seen before. Windmark also reveals to Nina that Michael is not a child but a "chromosomal mistake" (the episode title is Michael's "anomaly" number) and was scheduled to be destroyed before he went missing. In response, Nina tells him that while the Observers may think they're evolved, their loss of human emotion has made them regress into the use of primitive instincts, making them lizard-like – even the way they tilt their heads is physiological evidence of it. Windmark, looking dark, has a lackey prepare Nina for a Hastings-level mind probe, but she lifts the guard's gun – AND SHOOTS HERSELF RIGHT IN FRONT OF WINDMARK. Oh, man. I hate to lose Nina, but tell me she's not going to get the most high-fives in heaven for that one.

When the Fringe team arrives on the scene, they find Nina's corpse, which threatens to break Walter more than anything that's happened up to this point, not that Olivia handles it much better. The team checks the security footage (nice for the Observers not to have thought of THAT trick) and sees the fateful touch, and also realizes that Nina must have hidden Michael in the lab. When they find him, Michael, seemingly once again moved by the force of strong emotion, this time Walter's, sheds a tear for Nina, so they have reason to hope that a new mind link will work. In the end, Michael touches Walter just as he touched Nina, and Walter learns, via a long montage, presumably, the same thing she did – that Donald was in fact September. And with that "buh?" moment, we take a three-week break, whereupon the show will conclude with three (one on January 11 and then a two-part series finale on January 18) final time-bending episodes.