Police office Daniel Gillespie is at a train station in Philadelphia and approaches a man in a black trench coat carrying a briefcase. Gillespie ignores his radio caller and tells the man to set the briefcase down. The man refuses and the monitor screens around the station fill with static. Gillespie screams in pain as his body starts to crystallize and then he explodes.
Olivia is trying to put on bowling shoes at Sam Weiss' bowling alley. He tells her to relax and not let the stress of her head trauma interfere, but Olivia says that she doesn't see the point because she can't even walk without a cane. Olivia wonders what he did for Nina and Weiss explains that he retaught her how to use her cybernetic arm to eat French fries. Weiss asks about her headaches and Olivia admits she hasn't had any yet. Weiss is surprised, and tells her that they're done for the night and she should come back the next day.
In the lab, Peter is trying to find an apartment that his father likes but isn't having any luck. Walter wants to stay at the hotel where they are but Peter wants to have his own room and not have to worry about his father doing naked jumping jacks. Astrid has discovered a report on the explosion at the train station and informs them that there was no trace of explosive residue. The team goes to the station and review the security recordings, but they were all scrambled just before the explosion. The station is covered with explosive detectors and it seems impossible that someone could have smuggled in a bomb. Walter finds pieces of red crystal among the debris while Peter finds Gillespie's bomb imbedded in a bench. As Broyles arrives to tell them that no one has taken credit for the explosion, Peter shows them the badge and concludes that Gillespie was at the center of the explosion. Walter determines that the crystal isn't crystal, but rather is organic residue. Specifically, it's someone's ear.
Walter takes all of the crystal pieces back to the lab and starts putting them together. As they work, Walter talks about how he went for a walk the other day, made a wrong turn, and found a restaurant that served great apple fritters. He's reluctant to explore new things but Astrid points out he wouldn't have found the apple fritters if he hadn't gone somewhere new.
Peter takes the records to his friend Slim Joe, who descrambles them and confirms that there some kind of high-frequency radio interference. At the lab, Walter shows them that he's reconstructed most of Gillespie and determined that there are needle marks between his toes. There are 47 of them and Walter is sure that they were not accidentally inflicted.
Olivia and Peter go to see Gillespie's widow. He served in Iran until recently and wasn't under medical care. Olivia gets a sudden headache and runs to the bathroom to vomit. Once she's done, she notices a loose panel beneath the sink and removes two metal cases. They hold vials of liquid and an injection device. Mrs. Gillespie admits she's never seen them before. As they leave, Olivia tells Peter that she believes Gillespie was still fighting some kind of war. When Peter asks about her headache, Olivia denies that it's a problem.
In Oak Park, IL, Diane Burgess slips out of bed in the night and goes to the bathroom. She injects herself with the same liquid that Gillespie had and watches as her skin briefly crystallizes. The next day, Diane meets with Colonel Raymond Gordon, who tells her that he's calling back to active duty. He tells her that Tin Man protocols are in effect and gives her an encrypted cell phone. Gordon tells her to take a plane to Washington D.C. and await further instructions.
Olivia meets with Weiss and tells him that the headaches have started. He warns that she's suffering from aphasia but her memory is starting to come back. Weiss tells her to start doing bowling scores to help restore her memories and learn some patience.
Walter confirms that Gillespie was receiving injections for at least a year, and that he was in Iraq when he started taking them. He believes that someone used a specific radio wave to activate the serum, causing Gillespie to explode. Astrid checks Gillespie's army file and learns that he was exposed to cyanogen while he served in Iraq, and was under the treatment of three Iraqi doctors. Olivia and Peter take the information to Broyles, who confirms that Gillespie was entered into Operation Tin Man and his identity and that of others exposed were redacted. Peter says he needs to go to Iraq and uses his contacts to find the three doctors. Broyles sends Olivia along to keep an eye on him.
Peter and Olivia arrive in Baghdad and met with Ahmed, one of Peter's old contacts. Ahmed isn't happy to see Peter and accuses him of looking after himself no matter the risk to others. Peter insists that he's trying to keep innocents from being harmed and that he cares, and Ahmed accepts him at his work. He leaves Olivia and Peter there while he goes out on the streets. Once he's gone, Olivia asks what happened to Peter in Iraq but Peter refuses to discuss it.
At Harvard, Walter injects the serum into a watermelon and tries to trigger the explosion process using radio waves. He gets the right frequency and the lights flicker as the watermelon explodes.
As they wait, Peter admits that he's been in and out of Iraq several times over the years. Ahmed returns and escorts them to Dr. Malik Yusef, who is working at a restaurant. Yusef refuses to discuss Tin Man until Ahmed assures him that he can trust Peter. Yusef explains that he treated American soldiers exposed to cyanogen and came up with a cure. However, the cure's side effect caused the patient to turn into a human bomb. Yusef warns that Colonel Gordon was the one who kept the program going and that he doesn't value human life.
Back in Washington, Broyles assembles his team and tells them that they've rounded up two of the three remaining survivors. However, Burgess is still missing after she took a plane to Washington. Colonel Gordon has disappeared and the Pentagon has disavowed him as a rogue agent. Once they find the unwitting Burgess, they plan to move in and jam Gordon's signal before he can kill Burgess. They get a report that Burgess has been spotted at Federal Center Metro Station.
The FBI sets up at the station and watch as she gets an encrypted phone call. Walter realizes that the station's anti-terrorist devices will jam any incoming signals so Gordon will have to be inside the station to send the activation signal. They have no choice but to let Gordon activate the signal and then track him. Broyles authorizes the operation but Walter warns them that they'll only have 30 seconds before Burgess "activates."
Gordon calls Burgess and gives her instructions to take a briefcase from a man in a black trench coat and then go back to the hotel for further instructions. Peter and Olivia split up to search the station and find Gordon. Burgess approaches the man with the trench coat and Gordon activates the trigger signal. Walter and the technician in the surveillance van discover that the trigger signal is jamming their equipment, and they can neither track it nor jam it. Broyles is unable to contact Olivia and Peter and orders the rest of the team inside. Burgess starts to crystallize as the man with the briefcase backs away from her. Peter finds Gordon and attacks him, and the colonel drops the transmitter. Olivia picks it up and smashes it with seconds to spare as the FBI agents capture Gordon.
Later, Peter is examining Gillespie's remains as Walter tells him that he's chosen an apartment near where William Bell used to live.
Olivia goes back to the bowling alley to see Weiss, who simply measures her hand for a bowling ball size before telling her they're done for the night. As he walks away, she snaps at him and draws her gun to point it at his head. Sam merely stares at her and Olivia realizes she's walked over to him without using her cane. Weiss tells her good night.
Broyles meets with Gordon in interrogation. The Colonel tells Broyles that he and the others he works with are up against an unseen enemy and decided to send them a message. The Pentagon refused to believe them when Gordon and his people warned that there were invaders from another universe. Gordon's people believe that the men in trench coats are couriers that are delivering information about this world's science and technology to their superiors as a prelude to conquest. Whatever is in the briefcases will destroy this world.
The surviving courier from the Washington station goes to a diner and gives his briefcase to… the Observer. The Observer opens it and examines its contents: photos of Walter.
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