Philadelphia Mutual Savings Bank. A team of five bank robbers storms the bank at night, killing the guard and disabling the security system. In command is MITCHEL LOEB ("In Which We Meet Mr. Jones"). The robbers proceed to the main vault and stretch a black tarp over the vault wall. Loeb gives the command for two others to fire a harpoon -- and it flies right through! Loeb and two others use the harpoon's cable pull themselves through the wall. They have a minute and forty seconds. Once inside, they quickly break open one safe deposit box, pull out a heavy box, and push it through the wall. As the men pull themselves back out, the last man struggles to loosen the harpoon. As he unhooks the harpoon and races to get back through the wall, it solidifies around him -- crushing him inside. With nothing left to do, Loeb pulls out a gun and shoots him in the head, leaving him half-stuck the wall.
Our team arrives at the bank to find the robber hanging out of the wall. Broyles says that two other bank vaults have been breached, one in Cleveland the other in Baltimore; now they finally know how. Each time the only thing that was taken was a single oversized safe deposit box. Suddenly, Olivia realizes she knows the man stuck in the wall: RAUL LUGO. She served with him in the Marines, and she's even been to his house and had dinner with him and his wife.
At the bank robbers' undisclosed hideout, one man attempts to open the deposit box they just stole, and Loeb announces they have one more box to retrieve. As Loeb injects himself as part of a decontamination process, another team member, RYAN EASTWICK, says they should have tried to save Lugo. Loeb tells the team that if anyone wants out, they can leave now. No one does.
Meanwhile, at Wissenschaft Prison in Frankfurt, Germany, DAVID ROBERT JONES ("In Which We Meet Mr. Jones") is greeted by his lawyer, MR. KOHL.
At a hardware store in Philadelphia, Walter and Peter shop for supplies. When Walter expresses amazement at the size and selection of the store, Peter reminds him that a lot of things have changed since he was locked away. Walter makes a wisecrack about Peter's failure to live up to his potential. Peter says that Walter, of all people, is in no position to criticize his life choices.
Back at the prison, Jones learns that the job in Philadelphia was a success. He tells his attorney to wire another hundred thousand dollars to Mr. Loeb and to give him the location of the next item. Jones also hands the attorney a list of items he will need at their next meeting.
Olivia heads to Edison, N.J., to question Lugo's ex wife, SUSAN. It turns out Raul moved out two years ago and Susan is unaware of what he's been up to. Olivia reminds Susan that they've met before; she came over once for dinner with her and Raul. Susan recalls the dinner, but doesn't remember Olivia being there at all. Instead, it was John Scott who with them that night!
In the bank vault, Peter helps Walter saw off Raul's hand. Walter believes that if he can examine the hand on a cellular level, he may get a clue as to how it was able to pass through a wall. Walter then explains that what we think of as solid matter is mostly empty space on an atomic level. But to actually pass through matter, the robbers would need cutting-edge technology. Peter asks Olivia if she has learned anything from Lugo's wife, and Olivia reveals that she apparently never met Lugo; it was one of John Scott's memories in her mind.
Massive Dynamic headquarters in New York. NINA SHARP learns the effort to retrieve John Scott's memories has hit a dead end. (Scott's body remains in the same oxygen chamber in which we saw him last in "The Ghost Network"). Nina reminds the tech they're in a race against highly motivated individuals, so every possibility must be exhausted.
At the Harvard laboratory, Walter demonstrates how the robbers got through the wall. Walter explains that the tarp found on the vault door was used to conduct a vibration on an atomic level, allowing the robbers to pass between the atoms. Using a beaker of uncooked rice sitting on top of a vibrating table football, Walter illustrates the process. He turns on the vibrating toy and places a toy action figure on top of the rice. The vibration allows the figure to sink into the rice. Walter has also concluded that use of the phasing technology can render the user radioactive, as indicated by the radiation signature of Lugo's severed hand. Olivia returns with news that all the safety deposit boxes were rented with cash over twenty years ago anonymously. However, a friend of Lugo's now tends bar in Boston, and Olivia and Peter head out to question him.
At the bar, Olivia chats up the bartender, telling him she's positive she has seen him before... at Raul and Susan's wedding! The bartender tells Olivia that Lugo went through a rough time after returning from Gulf War II, even spending time at a VA hospital. Olivia calls Broyles and asks to find which VA hospital Lugo was at.
At the hideout, the bank-robbing team plays chess while discussing a map of Loeb's they found of Germany. They are unsure what it means. Loeb then enters the room and informs them it's time to move out. The next target is a bank in Providence, Rhode Island. As they leave, Eastwick notices his hand is shaking -- something's not right.
Peter shows Olivia a few card tricks at the bar. Then Olivia shows a trick of her own: she can remember the order of all the cards in the deck after one look. She has an uncanny memory for numbers. She rattles off childhood friends' phone numbers, locker combinations, finally listing the numbers of the safe deposit boxes that were stolen: 233, 377, 610. Peter stops her -- those numbers are familiar --Walter recites them every night as he goes to sleep! They rush to Walter's hotel room. Peter asks Walter to explain the significance of those numbers. Walter explains that they are part of the famous Fibonacci sequence. Then Walter realizes: "The safety deposit boxes are mine!" And he knows there are more boxes out there, but he can't remember how many, or where they are, or what is in them.
At Massive Dynamic, the technician has managed to access the last part of John Scott's memory -- an image of Olivia. Somehow they must have shared consciousness and switched memories ("Pilot"). Nina realizes: the memories Massive Dynamic wants may now be in Olivia's mind.
VA hospital, Washington D.C. Olivia asks if anyone remembers Lugo and who he hung out with. One of the orderlies remembers that Lugo was part of a group they called 'the Chess Club.' He gives Olivia the names.
At the FBI, Charlie and Olivia track down Lugo's three other chess buddies. One of them just bought a ticket to Providence, and the plane landed 45 minutes ago. Peter tricks Walter into remembering the bank he used in that city, and the race to stop the robbers is on!
In Providence, the FBI has shut down the streets surrounding the bank, and the bank manager takes Olivia and Charlie to the vault -- where they discover the deposit box has already been opened. Olivia realizes the robbers must have breached the vault through the floor -- and now they're in the sewer system. The FBI agents rush outside to find the robbers getting in their van. Olivia shoots Eastwick in the leg before he reaches the van, foiling his escape.
Back at the hideout, Loeb shows the remaining team what they're stealing: parts of a highly advanced device, for which they just retrieved the last piece. Loeb then makes a phone call: "He's coming tonight."
In the German prison, Jones takes the items he requested from the attorney: suntan lotion, a wad of US currency, eye drops, and a vial of pills. He then asks the attorney to return at 6:30 a.m. for Jones to sign the paperwork for his appeal. And one last request: he slides a drawing of Olivia across the table.
Back at the FBI office in Boston, Eastwick is in custody. As Olivia tries to break him in the interrogation room, Eastwick repeats his name, rank, and serial number. Peter notices Eastwick's hand is shaking, and asks Olivia to step out of the room. Peter explains to Eastwick that he has radiation poisoning and, if left untreated, will die. If he wants help, he'll have to tell Peter who hired him and what he was stealing. Eastwick doesn't know who or what, but he remembers overhearing a conversation about a field in Westford. Olivia recalls that Mr. Jones wanted the name of a location in Westford -- Little Hill ("In Which We Meet Mr. Jones"). The FBI springs into action.
In the Harvard lab, Walter begins to remember what he was trying to hide in the safe deposit boxes. When Peter was a little boy he contracted a very rare disease, a form of bird flu. Walter became consumed in trying to find a cure. In his research he found the name of a doctor who died in 1936 who had some success in treating the disease. So Walter designed a device to reach back in time and bring the doctor back to save Peter. Walter believes this is the device he has hidden in the deposit boxes. Peter asks if he used the device, if he really went back in time. No, Walter says, he never used it; Peter was able to recover on his own. But the science behind the device is real. In theory it could retrieve anyone from anywhere.
As Olivia races to Little Hill, Loeb and a team of surveyors set up a number of devices, triangulating a specific coordinate. Meanwhile, Jones snaps his Attorney's neck and puts on his suit. And as Olivia nears the site, three black SUVs that run her off the road. She jumps out of her car and takes off running, but before she can escape, her pursuers hit her with a tranquilizer and she goes down.
Back at Little Hill, Loeb's team finishes setting a ring on the ground. They step back as it begins to glow. In Germany, Jones takes the eye drops, applies the sun block, and stands in the corner of his cell. And as a bright flash of light envelops him... he appears in a column of light inside the ring at Little Hill!
Broyles calls Nina and tells her that Olivia has been abducted. Nina shows genuine concern for Olivia's safety and offers her full support in finding her.
Loeb welcomes Jones and informs him that they have Olivia. Jones smiles. "Then let's not keep her waiting."