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The episode begins with Peter Burke telling Neal that only one person could have been involved with Flynn's transfer, and death. That one person is a senator; Senator Terrence Pratt. Turns out the senator use to be a police officer during the same time as Sam (James, Neal's father) and Ellen. Peter and Neal then began their investigation into Senator Pratt’s involvement with a ring of corrupt cops working for the Flynns; which led to the framing of Neal’s father.
Senator Terrence Pratt is invited to the FBI office under the guise of discussing his knowledge of the Flynn family, from his days as a cop. However, he sees right through the ruse, and gets flustered.
Neal went to his desk, near where the senator's assistant is sitting. Neal calls her posing as someone from Bloomberg news asking her when they can schedule a meeting with the senator. Neal asks her to hold, then went toward the assistant pretending to get coffee. He gestured to her, offering her more coffee. She accepted and as she waited on hold for Bloomberg Neal, actual Neal sees the senator's schedule for the week over her shoulder.
Neal soon gets the evidence box from Ellen's death and in it he finds a key and asks Mozzie to figure out what it goes to. He begrudgingly agrees with the help of his friend, The Key Master.
Next, Peter returned to Neal, and they discussed how the senator knew what was going on in the investigation. Peter returns home to Elizabeth, and the boss shows up at his front door. Peter told him about the case and bringing down Pratt, and he warns Peter that Pratt is a well connected man and he should watch out.
They figure out Pratt's scheduled to get a shave, so they plant the crew in the barbershop and manage to add a tracking device to his phone and camera to his briefcase.
While Pratt was traveling around the city, he stopped at a construction site, which was an unscheduled stop. It turned out, Pratt uses the construction company, run by Cole Edwards, to funnel money into his project, and they in turn donate money to the senator.
Mozzie and Clinton went to visit one of Mozzie's connections, the Key Master. Mozzie told him he works only in riddles and through barters. The connection gave them a riddle, "Rome Rome a basket took him far from home, in the dessert he is the sun" and told them to come back tomorrow. Clinton immediately thinks it is referring to Moses, but Mozzie says that was too simple.
Neal and Diana, during Mozzie's deal were in the office figuring out how to get Pratt, when they call Peter while he was driving. He said he knew how to get Pratt, then realized the brakes weren't working in his car. Peter was then hit by a car in an intersection.
At the hospital, Elizabeth confronted Neal about how dangerous the situation is, and begged him to keep Peter out of this by lying to him. She demanded that he continue the investigation without him.
Mozzie, meanwhile, was trying to figure out the riddle, and decided to meet with Neal for help. Diana also called Neal during the meeting to tell him about what Peter found. Turns out Pratt made forges of paperwork for Edwards construction company to cover up the fact that Edwards is ordering very expensive materials, then changing the order for the cheapest kind of materials, keeping the extra money and paying off people to keep it quiet.
Mozzie continued to talk about the riddle with Neal, who thinks it too refers to Moses. Turns out it Moses means son in Hebrew and the Key Master wanted Barney, a doll head of Mozzie's.
Neal then meets with Edwards undercover, insulting all his work, introducing himself as William Gregg, a professional from abroad. Edwards was building a new skyscraper. Meanwhile, Diana warned Neal that Pratt was entering the building getting ready for a meeting with Edwards. She runs outside to say hello to Pratt, saying she remembered him from the barbershop. She tried to distract him; saying she could be his stylist. Neal told Edwards he needs the best materials for his new building, "you been to the coliseum lately, the Romans don't skimp." Neal then quickly sneaks out, just as Pratt reaches the office.
Next, the Key Master tells Mozzie and Clinton that there is nothing special about Ellen's key, it's just ten years old. Clinton left the meeting, but Mozzie stayed. The Key Master asked him for the real key, realizing Mozzie tricked him. Mozzie called Neal telling him the Key Master came through. Clinton goes back in and demanded to be told what is going on.
Back at the hospital, Peter has Clinton set up a work station in the hospital room. Clinton told Peter about the duplicate key, saying Neal had something to do with it. Before Neal can visit Peter, Elizabeth says she meant what she said yesterday, and to keep Peter out if it. Neal told Peter that the Key Master said the key turned out to be a dead end. But Peter knew Neal was lying to him. Peter told Elizabeth that Neal is lying to him, and she says nothing.
Diana said that the changes Edwards planned for the project were going to happen, so they intercepted his call, and had Peter pretend to be a construction supplier. They bring Edwards into the office, and the boss told him he could have 25 years in prison for the fraudulent changes or they will make a deal to bring down Pratt.
Pratt was being interviewed about the arrest of Edwards, and commented that he doesn't tolerate corruption. As Pratt was walking to his car, we the viewers see that Peter and Elizabeth are watching all this though the secret camera still on the briefcase. Neal is shown confronting Pratt.
Neal confronts Pratt about the involvement with Edwards. However, Pratt replied that Neal's father was the criminal posing as a cop. Neal threatened to find out what is happening. Pratt replied that the chance to do such was nonexistent because there was already restructuring occurring at the FBI office, and we soon find out that the boss is being forced out of his position because of Pratt's political connections.
It was very somber as the boss, Hughes, left the FBI office for the last time, he told the team "no one could ever ask for a better team than I found in you."
Peter told Neal this means business, and they will take down Pratt.
Neal and Mozzie discuss the key, giving him another riddle, saying the key isn't a key, it's a guide. The key shape creates a silhouette of the Manhattan skyline, pointing them to a location. Meanwhile, Peter and Clinton are discussing the same thing. The episode ends abruptly.
The next episode is titled, "Empire City."