At Harvard, Walter is checking Bell’s mental responses while he’s still in Olivia’s mind. Peter is icing the vegetative body that they’ve found to transfer Bell mind into. They go ahead but the transfer fails. Afterward, Peter reminds Bell that he promised to leave Olivia’s body after 48 hours. Olivia suddenly takes control of her body and asks Peter for help, and then collapses. They take her to the hospital and the ER doctor prepares to treat her, but Walter warns that Bell’s presence may have altered Olivia’s physiology. As they prepare to revive her, Bell stops the doctor and warns that the procedure will kill Olivia’s body.
Later, Broyles arrives and Bell admits that he didn’t anticipate that the lost of consciousness would occur so rapidly. The scientist reluctantly admits that in each case in his tests, he was unable to recover the lost consciousness. However, Bell explains that Olivia can’t survive without his presence, and warns that she doesn’t have more than a day before her consciousness is lost. They go back to the lab and try to find a way to pull Olivia out, but nothing seems likely. Bell suggests that they try and find a way to go in.
Meanwhile, Peter talks to Astrid and wonders if Bell is willing to risk Olivia to stay alive. Walter and Bell come in and suggests whole brain emulation, which will let them put Bell’s consciousness in a computer. They believe they can use the same process they used to put Olivia’s mind into John Scott’s memories, but Peter notes that it required an electromagnetic probe and hallucinogenics. Walter agrees and suggests they use LSD, and Bell agrees. Walter wants Peter to come along since they will be exploring Olivia’s subconscious, and Peter knows her better than anyone.
Once the LSD is ready, Peter, Walter, and Bell take doses. As Broyles arrives, Peter’s dose takes affect and he notices that Broyles is bald. They begin the transfer and Peter finds himself on a city street. He spots Walter, who is atop a bus. Once Walter falls down and Peter catches him, they realize that Bell isn’t there. Walter admits that now they just have to figure out where Olivia is. They start searching, and notice that everyone is dressed like Olivia because it’s her consciousness. They see a flashing light from the Twin Towers and Walter realizes that it’s a SOS. He uses a pudding cup foil to flash back a message asking who it is, and the sender says that she’s Olivia.
In the real world, Astrid monitors the others and prepares the computer for Bell. Broyles starts to become fascinated with licorice, and Astrid realizes that he’s touched the LSD.
Walter and Peter spot Olivia’s stepfather watching them and Walter has them hide. All of the pedestrians stop moving and fixate on the Bishops, and Walter says to run. Everyone chases after them, and Walter gets into a cab. Once Peter is in, Walter drives away, evading pursuit when two cars come after them. They get to the Twin Towers and find Nina waiting for them. She offers to take them to Bell’s office, where the light signal came from. Nina escorts them to the fastest elevator but she uses her cybernetic arm and Peter realizes that it’s a trap. He pulls Walter back before he can enter the empty shaft, and Nina tries to push them in, overbalances, and falls to her death.
The Bishops take another elevator and arrive at Bell’s office. Going in, they find Bell, who is a cartoon. When they ask why he’s a cartoon, he points that they are as well. He explains that he lied and claimed he was Olivia because he didn’t think Peter would risk coming there otherwise. Bell tells them that he was almost run down on the street and came to his office for safety. He believes that Olivia’s sense of self has become confused, initiating the darker side of her subconscious. Peter figures that she is retreating into her subconscious, and Bell warns that if she’s hiding, they have no trail to follow to her. After a moment’s consideration, Peter suggests that Olivia would go to the safest place she knows to hide.
Astrid continues her work and brings some food for Broyles, who is still tripping out and asks her to hold his hand.
Peter, Walter, and Broyles go to the roof where a zeppelin is moored. Peter suggests that they go to Jacksonville, the last place she thinks anyone would look for her. Hundreds of people surge into the building and zombies come out onto the roof. Peter holds them off and unties the zeppelin, then jumps off the roof and grabs the ladder just in time.
En route to Jacksonville, Walter admits to Bell that he needs his help. However, his old friend tells him that when they were younger, they needed one to balance the other. Now that Walter is older and wiser, his decisions will be just. A fuel alarm and Peter goes to investigate. He finds a locked room and opens it, and a man with a black X on his chest bursts out. He threatens to shoot Peter with a flare gun, grabs a parachute, and then asks his name. Once he gets an answer, the man says it’s nice to meet him and then shoots open the side of the zeppelin. Walter is sucked out and tries to grab the man, but fails and crashes to Earth.
In the real world, Walter wakes up from the shock.
Bell and Peter arrive in Jacksonville, and Bell says that the man was someone unpleasant from Olivia’s past. He prepares to go to the daycare center, but Peter says that Olivia would have gone somewhere else. They take a motorcycle to Olivia’s location.
Walter and Astrid work on the computer but Walter breaks one of the tubes. He cannibalizes his record player for parts.
Peter drives to the military base where Olivia lived as a child. He explains that she always wanted to feel normal, and was at her best the day before Walter and Bell began testing. All of the houses are the same, but Peter says that Olivia’s father painted the door of his house ride. They finally find the house and Peter goes inside, reverting to normal appearance. A young Olivia and her parents are there, and the adult Olivia comes over to greet Peter. When he looks into her eyes, Peter says that it’s not here. Young Olivia comes over and says that she needed to know it was really him, and she knew the real Peter would recognize him. Peter takes her hand and Olivia’s parents disappear. They hear footsteps and Olivia’s stepfather comes after them.
Peter grabs Young Olivia and runs outside, becoming cartoons, and the army closes in on them in hummers. Young Olivia falls behind and Peter shoves himself out of the way. He’s run over and wakes up in the real world. Walter says that it’s up to Bell and they can’t get back in quickly enough to do anything.
The soldiers, led by Olivia’s stepfather, close in on Bell and Young Olivia. She tells them to stop, saying she’s not afraid of them, and they freeze. Young Olivia becomes her adult version, and Bell explains that Olivia has never felt safe, He says that Walter is ready to transfer his consciousness, and gives Olivia a message for his friend: he knew that the dog wouldn’t hunt. Bell and the others disappear, and Olivia wakes up in the lab. Walter performs the transfer and confirms that Olivia’s consciousness is the only one in her body. However, Astrid determines that Bell’s consciousness didn’t survive the transfer. Olivia gives Walter Bell’s message, and Walter realizes that his friend knew that he wouldn’t survive the process.
Later, Walter is in his office mourning his friend. Astrid offers to cheer him up, but Walter says that he wants to be alone for a while.
Olivia is at home, sketching, when Peter comes to see her. They hug and wonder they will have to deal with next, and Olivia says she’s not afraid of moving forward. Peter notices her sketch, of the man with the black X from her consciousness, and Olivia casually says that it’s probably the man who is going to kill her.
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