Why would someone choose to become a monster? That's sort of one of the central questions of Fringe, throughout its run, and last night's episode explored it in a slightly different way. The central conceit of the episode is that our team investigates a case that they already looked into, in the previous timeline, but once they delve beneath the surface, everything is totally different. But really, it's about what you're willing to give up to become something new, and what could make such a transformation worthwhile.
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To some extent, this is a bookend or companion piece to season one's "The Transformation," in which a man turns into a weird porcupine monster. "The Transformation" was really about the fact that Olivia had her ex-boyfriend, John Scott, living in her head, and she was having his memories and being consumed by thoughts of him — until she finally let go of him.
This time around, Olivia's in a comparable but different situation — she's got memories of a life with Peter that she didn't actually experience, and she's being consumed by thoughts of Peter. But Peter, unlike John Scott, is alive, so there's the possibility that this will go someplace.
Olivia's next family reunion will be really weird, and I kind of hope we get to see it. In this timeline, Olivia's sister is still married to the creep, and she has two kids instead of just one — which means Olivia has a nephew she has no memory of. One wonders if the fact that Olivia shot her dad in this timeline means that Ellie has a different set of daddy issues. (Whereas Olivia, who no longer remembers killing her dad, now no longer has that sense of closure.)
And because Olivia has lost her memory, she's been sent for psych evaluation and suspended from duty — which stops her from investigating the latest case for about five minutes, especially since she has special knowledge of this situation thanks to her incorrect memories. (Actually, it might have been more interesting if there was a case which Olivia ought to have known a lot about, because she'd investigated some aspect of it previously — but thanks to her Peter-centric memory revamp, she's less helpful than she ought to be.)
To some extent, the episode juxtaposes Olivia's decision to have 40 percent of her memories be at variance with the real world with a bunch of people deciding to become flying porcupine people. Although it's not ever really made explicit, the way the parallels between A and B story often are on Fringe — and I don't think the episode is suggesting that Olivia's choice is akin to becoming a mute creature in a cage on board a cargo ship full of monsters.
So what does taking control of human evolution even mean? The episode is full of hints that there's a huge conspiracy, or secret society, with the cuneiform tattoos and stuff, based around the notion of taking control over evolution. Which, of course, is a random process that takes place over long periods of time in response to external duress. It's like saying "We're going to take control over erosion by dynamiting a mountain."
Anyway, the episode's main plot feels somewhat inconclusive, probably because it's intended to set up something further down the line. The porcupine conspiracy is somehow connected to David Robert Jones' the season's uber-villain, but we don't really get any details about that, nor do we find out much about the boat full of monsters that we glimpse at the end of the episode.
Oh, and not only is Olivia fully committed to Peter at this point, but Walter has come around to seeing Peter as the closest he's ever going to get to having his son back. He pulls out the giant box of presents he got for Peter on all of his birthdays since his son died — leading, of course, to lots of shots of Walter wandering around with a copy of HUMP Magazine.
But in an episode full of people who are choosing to become monsters — like the couple at the end, who see it as a great adventure they're taking together — there's Lincoln Lee, who chooses not to be a monster. First of all, when he's driving around with Peter, and Lincoln makes a conscious choice not to be a jealous dick or blame Peter for Olivia's transformation. Lincoln makes a huge choice to be a good guy, whatever it costs him — and it nearly costs him his life, because he gets infected with porcupine-itis because he won't call for backup and get Olivia in trouble.
Later, Lincoln chooses to stay in Walter's lab and deal with all of Walter's poking and prodding, and gets saved from undergoing a transformation of his own. It's hard not to think, in some way, that Lincoln is being rewarded for his choice not to be a judgmental dick earlier in the episode.