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Fringe's opening weirdness takes place in Philadelphia, where two city cops are on a coffee run. As one of the officers heads off to pick up their order, the other receives a cell phone calling. He recognizes the number and refers to the caller as "Colonel."
The Colonel tells the cop, "It's time" and tells him that there will be someone in a black trenchcoat carrying a black briefcase as Suburban Station, a train depot. The cop, a worried look on his face, speeds off, leaving his partner standing in the crosswalk. At the station, the officer, ignoring radio calls from his partner, searches for his target. He finally spies him heading down the stairs (Colonel probably should have just described his awful ponytail instead.
Would have made things much easier). He stops the man and demands the briefcase, even pulling out his gun. As the Arrival and Departure screens in the station flicker, the officer grabs the briefcase from the man. Upon contacting the case, the officer begins to crystallize and then shatters into a thousand shards in the middle of the station.
At the bowling alley, Sam Weiss is coaching Agent Olivia Dunham on...how to tie her bowling shoes. Sam reveals that he once taught Nina Sharp another simple task: how to eat french fries. Agent Dunham protests, but Weiss calls her out on not sleeping. He again asks her if her headaches have begun yet, and then tells her they are done for the day.
Back at Harvard, Peter and Walter Bishop are in the lab trying to find a new apartment for the two of them. Walter, apparently a fan of the morning sun, needs an Eastward-facing apartment. Walter lets Peter know that "a good morning sets a tone for the day." Unfortunately for Peter, Walter's morning began with nude jumping jacks and opera arias. Perhaps Astrid would like to become roommate #3; she remarks that Walter has a nice voice.
Astrid, on the other hand, has a nice eye: while searching the web for unusual cases, she comes across the Philadelphia incident, which officials are calling a bomb attack. However, despite 11 dead and nearly 30 wounded, they cannot find a single trace of explosives. Almost giddy, Walter asks, "Shall I get my coat, Peter?"
The Suburban Station is a mess of torn bodies. It appears that whatever caused the carnage did not set off any of the terrorism alarms the station had installed. The cameras were not able to pick up anything more than static. As Walter pours over one of the dead, he discovers a crystal shard which he believes to be shrapnel from the explosion.
Agent Philip Broyles arrives on the scene to let Agent Dunham know that no terrorist groups have claimed responsibility. Sharp-eyed Peter brings the pair a badge he found on the scene, belonging to an Officer Gillespie - but there were no police officers wounded in the attack. Walter interrupts to say that the crystal he found was not a crystal at all, but organic material - material that resembles a human ear. "Well," Peter says. "I think Walter might have just found Officer Gillespie."
Back at the Harvard lab, Walter and Astrid perform autopsies to search for clues in the bombing. Walter asks Astrid where she lives, and he confides that he does not want to move because he has everything he could want in his current location. Meanwhile, Agent Dunham and Peter tries view the blurred security tapes from the train station, with help from one of Peter's contacts. However, the contact cannot clear the static from the screen.
Walter has been able to bring clarity to one issue, though: with Astrid's help, he has partially reconstructed the body of Office Gillespie using the shattered shards left in the bombing victims. Walter has found 47 needle marks on the dead officer, believing that he injected himself with a compound that would crystallize his body,thus becoming a bomb.
Agent Dunham and Peter interview Officer Gillespie's widow. As they discuss his tour in Iraq, Agent Dunham begins to shake and starts having flashbacks to her visit to William Bell on the Other Side. She rushes to the bathroom and kneels in front of the toilet, and the visions stop. However, she notices some loose tiles underneath the sink, behind which she finds Officer Gillespie's injection kit. On the walk to the car, Dunham deflects Peter's inquiry about her headaches.
We watch as a woman wakes up in the middle of the night. She sneaks out of bed, careful to not wake her husband, and enters her bathroom. From behind a secret panel, she pulls out an injection kit. She injects herself between her toes - just like Walter surmised Officer Gillespie did - and her foot momentarily crystallizes. The woman is next seen loading groceries into her mini-van when she is approached by a man whom she calls "Colonel." We recognize his voice from the other end of the phone call with Officer Gillespie. He calls the woman Captain Burgess and says that he is calling her back to "active status." He gives her a cell phone and an itinerary - the Colonel sends the Captain to Washington, DC. He tells her that "Tin Man parameters are in effect."
Now that her headaches have arrived, Agent Dunham goes to see Weiss. He tells her that it's a sign that her memory is on its way back. He then tells her that she's going to score a kids' bowling party. Man, I totally could have been an FBI agent.
As Walter, Peter and Astrid eat, Walter reveals that Officer Gillespie must have been injecting himself with the serum while still in Iraq. As Walter worries about their cow watching Peter eat his cheeseburger, he explains that the Officer would have needed some kind of trigger to set himself off. Astrid finds Gillespie's Army file - according to the file, his entire unit was exposed to a chemical weapon that should have killed them.
The file contains a reference to Project Tin Man, a classified experimental military project. Agent Dunham and Peter meet with Broyles to discuss Project Tin Man. They determine that they need to find three Iraqui doctors associated with Gillespie's unit, but that such a search would take weeks. Peter says that with just a few things - $20,000 and a fake passport among them - he can get into Iraq and meet with another contact who can find the doctors. The three, fearing that Gillespie was not an isolated event and knowing that they do not have weeks to wait for answers, decide to send Dunham and Peter to Iraq. Road trip!
In Baghdad, Peter and Dunham enter a darkened hookah bar. Peter meets with a man whose face is a shamble of scars. Peter asks the man for his help finding the doctors; the contact, Ahmed, spits back that Peter only cares about watching out for himself, and refuses to help. Peter begs him, explaining that many lives could be on the line. Ahmed agrees to look into it.
Meanwhile, Walter and Astrid experiment with the serum, using a watermelon and radio waves to see if they can recreate the explosion. The experiment works, leaving Astrid - who had just cleaned the lab - to proclaim, "No more fruit, Walter."
While waiting for word from Ahmed, Peter and Dunham drink at the bar. Dunham tries to pry information from Peter about his stay in Iraq. Ahmed returns before Peter reveals any particulars, and takes them to meet one of the doctors, now working as a cook because his people consider him a traitor for working in the American-run program. When Dunham mentions Tin Man, the doctor becomes nervous and initially claims ignorance.
The doctor explains that he was trying to find a way to neutralize the chemical weapons Gillespie's unit was exposed to. The doctor reveals that three others, in addition to Gillespie, survived the chemical exposure. They realized that the serum turned people into bombs. The doctor says that a Colonel Raymond Gordon, "a vicious man", argued that the program should be kept going but it was shut down. As the doctor explains this, we see Colonel Gordon watching Captain Burgess leave her family for her trip to DC.
Agent Broyles briefs a larger group about the potential bomb threat. They determine that Captain Burgess is the bomb and that Colonel Gordon is the detonator. Dunham explains that Captain Burgess most likely does not know that she's going to be used as a suicide bomb. The FBI locates Burgess, again heading into a metro station. The FBI watches as Burgess receives a phone call, but cannot locate the Colonel. The FBI decides to let Burgess enter the station to give themselves a chance to locate Colonel Gordon.
Inside the station, Colonel Gordon calls Burgess and tells her to take a briefcase from her contact, a man in a black trenchcoat (no ponytail this time, but still bad hair). Realizing that Colonel Gordon is not the contact, the FBI attempts to jam the signal to stop the explosion. However, they are unable to do so. Peter spies Colonel Gordon as Captain Burgess begins to crystallize. Peter tackles him, causing his detonator to scatter across the floor.
As Gordon and Peter tussle, Agent Dunham destroys the device, stopping the Captain's crystallization. The FBI swarms in and arrests the Colonel, saving him from a brutal beating from an enraged Peter. Walter watches it all unfold with glee from the surveillance van.
Back at the Harvard lab, Walter approaches Peter with a suggestion for a new apartment. At the bowling alley, Agent Dunham has grown tired of Sam Weiss's slow recovery program. As Weiss stands at the edge of the lane, preparing to bowl, Dunham pulls her gun on him and demands that he fix her. With a nod of his head, Weiss points out that Dunham is walking without her cane.
Agent Broyles interrogates the extremely creepy Colonel Gordon, who claims that "the enemy is among us and nobody's doing anything about it." He said that his group had to send the enemy a message with their bombings. He tells Broyles that "they are here, collecting data, making observations." He says that "they" are planning for war, and the briefcase contains data and information they've been collecting to use against us. Colonel Gordon admits that he does not know who "they" are, but he knows that whatever is in those briefcases "is going to destroy us all."
As he speaks these chilling words, we see the man with the briefcase from the train stations drop it off at a diner. He gives it to The Observer, who opens the case and flips through surveillance photos of Walter as the episode ends.