The episode begins with Neal and Sam discussing about the box while looking at the Empire State Building. The two have a heart-to-heart and Neal recollects moments from his childhood and Sam then tells Neal that he wants the box so badly because he wants to know who Sam really is. That would then help him figure who he really is too. Amanda comes into Peter’s office and tells him that she had a chat with Pratt and he told her everything. She also knows about the box Neal and his father are looking for and tells Peter to find the box before anyone else so they can find out, who between Sam and Pratt, is telling the truth.
Next morning, Peter meets Reese at a restaurant and Reese makes him hear a recording of a phone call his friends at the NSA intercepted between Pratt and Amanda. On it, Amanda is heard telling Pratt about the box and Pratt says he will be in DC by the morning. Reese says Peter has to get to the box before the FBI and Pratt can and suggests Peter takes Neal’s help to do it. Peter calls Mozzie and Sam to Neal’s apartment and then tells them that within the next two hours an FBI team will begin looking for the box in the Empire State Building, so they need to get to it before that.
Peter says Amanda doesn’t know which floor the box is in and he will be heading the FBI team and can control it and then asks Neal how long they will take to find the box. Neal doesn’t have a plan so he doesn’t know. At the office, Amanda briefs Peter and team about the box that needs to be searched for and found in the Empire State Building. She also says she has received some new intel and so the team will be searching floors 33 through 61. At home while thinking up a plan, Neal, Mozzie and Sam have some Champagne and the rising bubbles of the Champagne give Neal an idea. At the office, the FBI agents are dispatched for the search and Peter asks Diana and Jones to slow down the agents as much as they can. He then calls up Neal and tells him that Amanda is sending in a large number of agents and it wouldn’t take them long to clear the floors.
Neal and team have formulated their plan and according to it, Mozzie will enter the building wearing the green uniform of a waiter working at the building’s cafeteria because it’s the same disguise the FBI agents are wearing. After acquiring the box he will hand it to Sam and Neal will be handling things from the 103rd floor. Mozzie later calls Neal and informs him that the FBI agents are moving though the floors really quickly and also, Senator Pratt has moved into the 51st floor of the building, but he has no idea he is so close to the evidence box. Neal meets Peter and he gives Neal the plans to 51st floor. He says Pratt has installed some high end security there, but Neal knows a way to get around it. Peter tells Elizabeth they can go to a restaurant of her choice to celebrate the next day, after he has arrested Pratt.
Mozzie leaves at Neal’s doorstep a device that can help him get around the security on the 51st floor and Neal and Sarah test the device, while indulging in some romance. Peter tells Amanda that he isn’t at all happy with Pratt moving into the building, but Amanda says Pratt is a private citizen who has leased the office for his charitable foundation so he couldn’t be stopped. She tells him to trust the system. Neal goes over with Sam once again about what his part in the plan is, including what each hand signal means. Sam and Neal then walk up to Pratt who is sitting on a park bench reading a newspaper, so he is close enough for his proximity card to be cloned, which can then be used to bypass the security on the 51st floor.
They buy time by talking about the box with Pratt, while Mozzie, who is standing at a distance, waits for the card to be cloned. After it’s done, he signals them to clear out. Amanda shows her team Sam and Neal’s photo and tells them to arrest the two, if they are seen anywhere near the building. Neal enters the building and just then, Peter warns him about Amanda’s instructions. A while later, Mozzie and Sam dressed as cafeteria workers, enter the building. Neal makes it to the observation deck where Sarah is waiting for him and after getting there he gets down on one knee and begins proposing to Sarah to get everyone’s attention. Right after the proposal a building official invites them to the 103rd floor to celebrate the occasion.
Amanda finds out by tracking Neal’s electronic leg brace, where he is and asks another agent to come along, so they can arrest him. Peter arrives to talk to Pratt and a while later Amanda arrives there with a few other agents and says Neal’s leg brace led her there, but Peter says Neal isn’t there. Pratt suggests they check Peter’s leg and it’s revealed that Peter is wearing the brace. Amanda tells him to hand over his gun and badge and Peter does as is told, but has a smile on his face. Neal and Sarah are on the 103rd floor and are discussing how their life would be, if they were married and had kids. Sam and Mozzie make it to the 51st floor and using the proximity card gain entry into Pratt’s office and Diana and Jones show Amanda a scan which reveals that they might have found where the box is.
Just then Pratt arrives there and says he wants to witness the whole thing, so the evidence is not tampered with. Mozzie and Sam are carrying out their part of the plan and Diana and Jones are hoping they got in. Mozzie and Sam find the box hidden underneath a tile on the 51st floor and the moment the remove the box, a part of the floor collapses and Pratt, who is on the floor below sees the two through the hole in the ceiling. Amanda immediately rushes upstairs with the other agents. Mozzie gives Sam the box and the two of them split up. Neal who is still with Sarah on the 103rd floor begins assembling a device hidden in the Champagne stand. Sam is caught by one of Pratt’s guys and he brings the box and Sam to Pratt. Pratt says Sam will be going back to prison.
Pratt then opens the box and sees that it doesn’t have the evidence and just then Mozzie meets Neal on the 103rd floor and hand him a small box which apparently has the evidence. Neal then places the box in a small remote controlled zeppelin he has made and keys in the coordinates. Pratt sees the zeppelin from the window and realizes that it’s flying away with the evidence and points a gun at Sam and says wherever it’s going he will tell him. Sam too picks up a gun lying nearby and just then Peter arrives and asks them to put down the guns, but instead Sam shoots Pratt, who dies. Peter says he will have to arrest him, but James points the gun at Peter and then makes a run for it. Peter remains near Pratt’s body and just then Amanda and the other agents arrive at the scene and arrest Peter.
He says it was Sam who killed Pratt and Amanda radios her agents to look for Sam in the building and then reads Peter his rights. Sam makes it out of the building and later arrives at Neal’s apartment where he sees Neal has already gone through the evidence and Neal says he knows that Sam shot his supervisor because he had found out Sam was involved with the wrong people, which is why Ellen arrested him. Just then, Diana calls Neal and says Peter is being charged with Pratt’s murder, so Sam has to come in and testify that he killed Pratt in self defense.
Neal asks Sam to testify to clear Peter’s name, but Sam isn’t ready to do it because he feels he might have to go to prison for this. He walks out despite Neal begging with him to do the right thing. Peter is being taken away by the agents and at home, Elizabeth oblivious to all this is getting ready for their dinner. The episode ends at this point.