Agent Dunham and the Bishops investigate the sudden appearance of a strange cylinder after an explosion at a construction site. She learns from an old friend that this is not the first time the cylinder has appeared and that it could disappear just as quickly. She also realizes that an odd looking man appears in several crime scene photos. It turns out that he is already known to the Government and has been dubbed 'The Observer'. Dr. Bishop has a special interest in the cylinder and tells Peter of their own special encounter with 'The Observer' years ago.
In Brooklyn, a bald man sits in a diner and observes an accident in a construction site. Broyles summons Agent Dunham and shows a mysterious cylinder that appeared in the site. Further, he explains that this cylinder appeared many years ago and an old friend of her had found it. While Dunham visits her friend. Dr. Bishop get rid of Peter asking him to buy tin foil and sedates Agent Farnsworth; then he hides the cylinder and meets the bald man. Meanwhile the killer John Mosley is searching for the cylinder and killing and torturing whoever might provide a clue of the location for him. When he abducts Peter, he uses a strange device to find the location of the cylinder that was unknown to Peter. What is the mystery cylinder?
A strange cylinder which is somehow connected to Walter and a man known as "the Observer" appears from the ground at a construction site.
A creepy bald man without eyebrows sits in a diner and orders a roast beef sandwich with raw meat, room temperature water and 11 jalapenos on the side. He watches construction across the street, using spy gadgets to get up-close readings of the crew. He takes notes in backward handwriting that resembles hieroglyphics. He puts the whole shaker of pepper on his sandwich and tops it off with hot sauce. He practically inhales the sandwich. He checks on the construction again. The walls of the diner start to rattle. The street shakes. A plume of smoke shoots into the sky from the site from an explosion. The crane starts to come apart. As people flee the diner the man sits casually and takes money out of his wallet. He puts on his hat and glasses and walks into the site, briefcase in hand. He makes a call. "It has arrived."
At the Bishops' hotel, the Dr. babbles formulas to himself - at 3 a.m. Peter (Joshua Jackson) takes exception. He goes to sleep in the tub.
At the federal building, Peter walks without clearance to find Olivia (Anna Torv). He's irked pops kept him up all night reciting formulas for his favorite beverages - naked (he likes the breeze). Peter tells her they don't need him there. He's just a babysitter. He's getting restless. Olivia tells him Walter (John Noble) has said if Peter leaves he won't help.
The Fringies show up at a warehouse as Broyles (Lance Reddick) briefs them on the construction incident. The cover story is it was a gas main rupture. He wants them to see what really caused it.
A silver egg-shaped two-foot tall metallic object sits on a table. It's making odd vibrations. It came from underground. Walter thinks he might know what it is, but he doesn't want to talk about it yet. Broyles says Col. Henry Jacobson oversaw the investigation in 1987 the last time one of these things showed up.
Peter tells Olivia this is his last case.
Walter wants to take it to the lab. When Broyles says no, Walter uses angrily says he'll only work on it with his equipment.
Olivia visits Jacobson (Nestor Serrano), a widower, in Roseville, Virginia. She asks about Quantico in 1987.
He shows her a picture of Master Sgt. Stewart Mallick. He was watching the motion censors on the base and one night they went nuts. They found the metal egg thing, also vibrating. 48 hours after they found it there was a huge, downward explosion. And it disappeared.
Harvard Walter puts censors on the egg, using a tuning fork to get it to hum a high-pitch squeal.
In a car outside the warehouse, a man gets out with a really big gun and blows away the FBI guard. The gun seems to shoot pulses of light or sound, blowing people backward. He storms into the lab, taking everyone out along the way. He asks the remaining lab geek where it is. Fade out ominously.
Olivia gets a call in the middle of the night. There's no one there at first then she hears John Scott's voice. She calls headquarters on her landline and asks for a trace. She's told there are no records of a call in the last three hours.
Back at Harvard, Walter marvels at the egg, which Peter calls "a gigantic metallic suppository." Walter talks about about Project Thor, a project to make an underground torpedo. Olivia looks at a photo from 1987. She sees creepy bald guy and recognizes him from surveillance footage from two weeks ago at the hospital (she's really good at Concentration).
The blaster guy from the warehouse shows up at Jacobson's house and blasts him.
Olivia shows Broyles the photos of creepy bald guy. He takes her to a secret room, covered in photos with him in every one. It took them a year to spot him. She did it in three weeks. There are pictures of him from all over. They don't know who he is.
They've recorded him at over three dozen scenes related to the Pattern. They call him The Observer (Michael Cerveris), because that's what he seems to be doing.
Broyles gets a call.
At Harvard, Walter is ramping up another noise experiment, but not telling Peter why. He's getting really irked at his dad's silence when Olivia calls to tell him about the attack at the warehouse. Walter guesses someone has come for it. They need aluminum foil, their lives depend on it. Oh, and also, Walter would like a root beer float while Peter's out. Peter leaves and Walter asks Astrid (Jasika Nicole) to hand him a syringe, which he jams in her neck.
Peter returns to an empty lab. Astrid is out cold, Walter and the egg are gone.
At Jacobson's house, Blaster guy has Jacobson strapped down, with censors jammed in his nose and on his head. The man flips a switch and Jacobson writhes in pain. The man tells him to think about something. He finally does. The man blasts him again.
At the diner, Walter gets his root beer float. He's joined by Creepy Bald Guy. They discuss floats. Walter offers to share. The man says he wouldn't taste much anyway. The man thanks Walter for hiding the beacon, Creepy can't touch it himself.
The Fringies man the phones, looking for Walter. Olivia gets a call. Walter was picked up walking the freeway median.
Peter and Olivia pay him a visit. He won't tell them where he hid it, he tells them. He says he has to keep it safe for another four hours. His friend agrees with him. His friend Creepy Bald Guy. Olivia wants to know where he is, while Peter thinks he's making it up. Walter calls Peter "small-minded" and tell him not to act like his mother. Peter thanks him, it's exactly what he needed. Guilt relieved. He can leave.
Olivia briefs Broyles.
At Harvard, Peter packs up his stuff under the watchful eye of the cow. He gets a call back. He's looking for work. He goes through files, finding a photo of him with his dad. Blaster Guy lurks in the dark.
Olivia looks at photos on her computer. Astrid calls, asking what happened to Peter. She's at the lab. She says there was a struggle there.
Peter is trapped to the same apparatus Jacobson was. He tries to tell the man he doesn't know whatever it is he's looking for. The man rams censors up his nose and puts in an earpiece. The man asks him what the most pain he's ever felt in his life, then he turns the dial and answers the question for him.
Olivia shows Walter security camera footage of Blaster/Torture guy. He thinks Peter will lead him to the cylinder, even though Walter didn't tell Peter where he put it.
Back on the torture table, Peter tells the man he won't tell him. But then he seems to, as the man hears him think Walter hid it. He ratchets up the pain and realizes where Walter's hiding places are.
The man drives his car to a cemetery. He gets Peter out of the trunk. They find a grave for Robert Bishop. The man tells him to dig.
Olivia pulls up, alone. Gun out, she investigates. The man has the cylinder. He hears a footstep. He runs off, leaving Peter. Olivia checks on Peter, then follows. He blasts her, but misses. Peter saws his ropes off on a gravestone. Olivia hits Blaster guy, who leaves the cylinder on the ground. She kicks his gun away.
The cylinder starts to make noise and then whirs and digs into the earth. Olivia looks down a deep, perfect hole. The Observer observes. He makes a call: "Departure on schedule."
Peter tackles him from behind. They stare at each other and Peter starts asking questions. The Observer spits them out as Peter says them. Then The Observer gets ahead of Peter, saying "do you really know my father? Did you talk to him this afternoon? Are you his friend?" Then the Observer shoots Peter.
Peter stands up. Not dead, Olivia is relieved to see when she finds him.
Francis (Kirk Acevedo) visits Walter. He's there to take him home, but first Walter wants to see Astrid. He apologizes "what I did to you was very untrustworthy of me." He says he was doing what was necessary to protect us all. He offers to let her inject him, too.
Olivia and Broyles meet at the hospital. The cylinder is gone. They ID'd the shooter, wanted for a double homicide. Peter signs himself out. He tells Olivia he's starting to buy into The Pattern. He says the man in the woods knew him and knew what he was going to say before he said it. He hates to admit it, but Walter might be right. Olivia didn't see the bald guy. She tries to dismiss what he saw as due to the torture, but Peter says he's not going anywhere until he gets some answers. She gives him his credentials. Civilian consultant to Homeland Security.
At the hotel, Peter tells Walter about his day. He says the strangest thing was he answered a question he didn't know the answer to. Walter tells him ideas can be absorbed through osmosis.
Walter starts talking about the night of the accident. Peter's mother was driving. Thanksgiving night. Their car went out on the ice and it cracked. Peter thinks his dad saved them both, swimming to shore. Walter tells him, no, they died that night. A bald man saved them, a man who felt no cold. He heard his thoughts and the bald man saying he might need a favor from him someday. This was that day. He knew he had to protect the capsule for them. Walter says he knows Peter must think he's insane. "Not nearly as much as you might think," says Peter.
Olivia returns home. She prepares a dinner of cereal with a Scotch chaser. She looks up to see Agent Scott (Mark Valley) standing in her kitchen. He says hello. The cereal bowl falls to the floor, shattering into a gazillion pieces.