Fringe/Recap/S03 E04

Season 3, Episode 4:

Do Shapeshifters Dream of Electric Sheep?
Senator Van Horn, part of the US Government group overseeing Fringe Division, is in a car accident and brought to the nearest hospital for emergency surgery. Newton, the Shapeshifters' leader, arrives and kills the doctors working on Van Horn, then attempts to get him out of the building. He is pursued by hospital security and Broyles, who is a friend of Van Horn's and had come to support him and his wife. When Newton realises he won't be able to get Van Horn out, he shoots the Senator in the head and flees: the bullet wound bleeds mercury.

The Fringe team, now with all the resources of Massive Dynamic at Walter's beck and call, investigate. Walter studies Van Horn's body and discovers that he's not entirely dead, and believes that if he can stimulate the Shapeshifter's neural pathways, he can find a theorised "second brain" that would contain data on Van Horn's mission and history. When they realise that the Van Horn Shapeshifter has genuine feelings for the real Van Horn's family, they bring Senator Van Horn's wife in to try and talk to the Shapeshifter. The neural pathways lead to a point at the base of the spine, but Walter can't locate the second brain.

Meanwhile, Fauxlivia contacts Newton to inform him that Van Horn is still alive. Newton activates a Shapeshifter sleeper agent, who'd been living with the family of a police officer for many years without orders, and tells him to kill Van Horn and then take on a new identity. The Shapeshifter is reluctant, and in a conversation with his "son", its revealed that the Shapeshifter has come to love the family as though it were his own, and he doesn't want to leave them. Nonetheless, he goes on the mission and gets access to the Massive Dynamic labs. He winds up sharing an elevator up to the lab with Walter, who realises that since William Bell designed the Shapeshifters, their biology may be based on the Stegosaurus (Bell's favourite dinosaur), which had a second brain at the base of its spine. When they reach the lab, the Shapeshifter knocks Walter out and cuts the "second brain" -- a data disc -- from exactly where Walter theorised it was.

The Shapeshifter returns to his home and finds Newton, who claims to have helped him in the process of getting a new identity by killing the Shapeshifter's "family". When the Shapeshifter is horrified, Newton realises the attachment that's formed and reveals that the family is still alive -- before murdering the Shapeshifter. As Newton leaves, "Olivia" and Peter arrive, having tracked the Shapeshifter, and they pursue and capture Newton. In a maximum security prison, Fauxlivia visits Newton and gives him a tab that he uses to commit suicide. At the end of the episode, Fauxlivia invites Peter to her apartment and sleeps with him.