In this episode, the Fringe team learns that Walter Bishop's old colleague, William Bell, has been in control of David Robert Jones' actions to collapse both universes in an attempt to create a new universe under his own control, and the Fringe team must make sacrifices to put an end to Bell's plans.
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Walter stated that the events of this two-part season finale essentially purged all remaining Cortexiphan from Olivia's system.
The Observer is featured in this episode.
Signage saying "Eden" on the exterior of Bell's waterfront warehouse in 'Brave New World (Part 1)' foreshadows his mission to create a new, pristine universe with new creatures in 'Brave New World (Part 2)'.
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William Bell removed pieces of Walter's brain at Walter's request as seen in flashbacks in "Grey Matters".
Walter made a similar comment in "Peter".
Walter shot Olivia in the head in "Brave New World (Part 2)" in order to stop her being used as a power source for Bell's new world. (Image 1)
Bell tried to use Olivia's powers to create a new universe in "Brave New World (Part 2)".
Walter sacrificed Olivia, the most valuable piece in the game, in order to save the world in "Brave New World (Part 2)".