Two computer hackers or "phishers" are trying to steal information from a bank while riding in their SUV. What they don't know is Charlie has provided Don's team with a tracing method to nail them, and they are captured.
At the Eppes house, the brothers are waiting for dinner to be delivered and watching a game on TV. When dinner arrives, Don is told by the delivery person that the credit card he called in with the order has been declined, Charlie offers to pay, but Don – puzzled because he just paid the bill – gives the girl another card, which is also declined. Alan pays the bill in cash while Don calls his bank. According to the information Don is given, his accounts are all empty. This becomes a bit clearer when he receives the text message "We have your money…"
Under questioning the two phishers reveal they had been running scams from a cyber café when two Russian-speaking men, Len and Alex, who work for some guy named Yuri, approached them. This draws in the LAPD Organized Crime Task Force and the return of Lt. Gary Walker, who fills the team in on the dangerous man behind the California branch of the Russian Mob Yuri Kovashenko.
Charlie and Amita are working on tracking down who stole Don's money, and more importantly, how as when Don's money is replaced the thieves could just take it again. As they work on a backscatter program to trace back to the thief, their conversation does reveal where Larry is in this episode, at a conference. But in typical Larry fashion, he has called Amita, confused about something… Where is he, Cleveland or St. Louis? Actually, he is in Minneapolis.
Don and Megan go the bank that was hacked to meet with the head of the IT department and his team (a young father and a mother-to-be) about the attempted theft. As they are talking to the bank employees, Don receives a disturbing call on his cell phone. The phishers were bailed out. Worse the bail system was hacked, and they were bailed out using one of Don's canceled credit cards and an anagram of Don's name. Shortly thereafter, the hackers and the girlfriend who picked them up are found shot through the head, their bodies dumped by the river like trash. It is a message from the mob, to back off. Charlie's backscatter program has yielded results: they have traced the source back to an Auto Repair Shop that is known to be a front for the Russian Mob. A joint FBI/LAPD task force leads a raid on the site while Charlie is showing the program to his class to demonstrate real world applications. A student notices an added line to the program; too late Charlie reads the message "We're waiting for you." He frantically tries to call Don who, standing in the empty garage, realizes it is going bad, as an explosion is followed by gunmen opening fire. In the chaos, David is shot in his shoulder. Charlie figures out the mob led them into the plot; setting up Don because they knew Don would call in Charlie and Professor Eppes would use a high-tech solution (that they could booby-trap) to try and catch them. Charlie explains this as "multi-player theory" much like football. Lt. Walker warns Don that he and his family could be at grave risk. Don tries to protect Charlie by lying to him that Don was removed from the case. Charlie doesn't believe his brother, even calling the FBI to ask for the lead agent on the case and is offered Don's voice mail. Charlie continues his work without his brother's knowledge. Returning to the bank, Don notices only the I.T. manager is there; his two associates are out (one with a sick kid, another "working from home"). Before he can question this any more, something has happened in Charlie's class. Charlie notices two Russian mobsters are sitting in the back of his class. Not wanting to alarm his students, Charlie has them figure out how to get help. With no cell phone signal, he has four of them go, using different paths, to bring back campus security. Soon, not only are the mobsters gone, campus security and the FBI are at CalSci. Charlie's office, with his backscatter work, has been disturbed. Suddenly, he becomes alarmed as he realizes the rest of his work is at his home office in the garage. He and Don rush home, Alan is safe and everything seems undisturbed, but Don finds a cigarette on the floor of the garage and none of the Eppes men smokes. Don becomes furious, lashing out at Charlie for continuing his work on the case, endangering not only himself but also their father. In truth, Don is scared that he may not only fail to catch the bad guy but his family could get killed as well.
Against Don's orders, Charlie continues to work the case. A wounded David starts to hang around the Eppes house, trying to protect Don's family. As David and Alan play air hockey nearby, David makes a comment on "fake outs", making Charlie have an epiphany. The mob has been intentionally misleading them, using the Eppes family to distract the authorities from the real target: the bank that was phished. Knowing Don will just cut him off, Charlie calls Lt. Walker to share his info. It is now all clear: stealing Don's money, bailing out (and killing) the phishers under Don's name, threatening Don's family was to keep the FBI from discovering the truth at the bank. So Don and Lt. Walker nab the bank's IT manager to get him to cooperate with them against the Mob, convincing him that his employees (who are not at home, but are being held hostage) will be killed if he goes along with the mob but not the FBI. The Russians' plot is to get an on-site hacker in the bank to get info to access the ATM system, stealing thousands of IDs and millions of dollars in a day. After getting (via the IT manager) the hacker's phone number, Charlie calls the hacker, taunting him. The hacker panics and calls Yuri, who tells him to keep working. Using a GPS, Don tracks Yuri to a location downtown, rescues the hostages, and allows Lt. Walker the great satisfaction of taking down Yuri with a great right hook.
David joins the Eppes for dinner, marveling over the "statistically possible but unlikely events." Don wonders if he should get Charlie to stop working for the FBI but Alan would rather that Charlie and Don keep connecting as they have been.
The episode ends with the two brothers teasing each other "Chuck." "How about if I call you Donald" "How about if I call you Nerd?" "How about….."