Bonnie Parks, a television news reporter is missing.
Charlie Eppes is being interviewed by different reporter about his help with the FBI and this particular case. Charlie explains how he uses math to help solve cases, and says he is there to help find the missing reporter.
Agents David Sinclair, Colby Granger, and Don Eppes are investigating the case.
Later, at Charlie and Alan's home, Don is furious. He sees the evening news with Charlie discussing his methods with the reporter. Alan tries to reassure him that Charlie mentioned no specific information about the case, but Don is still upset because, as he says "That is the Cardinal rule. You do not discuss an ongoing investigation with the media!" He says that the director of the FBI is also unhappy.
Charlie decides to leave and go back Cal Sci, to finish some work. As he is driving, he notices a large pick-up behind him following too close. He gets a little annoyed and pulls over to let the pick-up pass. The truck pulls over behind him. Charlie pulls out, and the pick-up follows. At this point, Charlie is getting nervous and tries to lose them.
The next day in Charlie's oom, Larry Fleinhardt and Amita Ramanujan enter and realize Charlie spent the night at the university. Charlie tells them about his apparent stalker, and both believe he probably just cut someone off, and they were upset.
At the FBI - Colby, David, and Don are watching some footage of the missing reporter work. They learn she was quite relentless and courageous when it came to doing her investigations. She was not afraid to take on large corporations or influential people.
Charlie enters and tells them about "Asymmetrical Threat Assessment", which he plans on using to help narrow down the suspected kidnappers.
Back to Eppes home, Alan has Ray Galuski (aka Ray Ray), another professor from the university working on a filter pump problem in the pond. Ray suggests some home improvements to make the house more environmentally friendly. Charlie thinks this might be a good idea, Alan is not so sure.
Colby and David check out Bonnie's office. They learn from a co-worker that Bonnie was extremely work focused, she had no personal life, and she does not trust computers. She feels they are not secure. They find some note pads that are blank, but can see some indentations from previous pages. David takes them to be analyzed.
Back to Charlie's garage, Charlie is working on his threat assessment. Amita comes in. Gives Charlie a kiss and asks why Alan is grumbling about Ray trying to ruin the house. Charlie must take his data to Don. Amita offers to ride with him, but he refuses.
Colby is looking at the last known footage of the missing reporter, a parking garage security camera. David enters, he had the note pads analyzed, there are two pages of numbers.
Charlie's car, he is a little jumpy about cars following him. But just as he calms down a bit, he passes the same silver pick-up from before. It begins following him. The truck hits him from behind and he crashes. A guy gets out of the pick-up and shoots at Charlie, shattering the driver side window. Charlie quickly crawls out the passenger side door and hides in some bushes before the man with the gun gets close enough to see he is no longer in the car. Charlie pushes the panic button on his key fob, and the horn begins to honk and the lights begin to flash. As there are others in cars paying attention now, the man jumps into the passenger side of the pick-up and speeds off.
Charlie is sitting in the open back of an ambulance when David and Don show up. Charlie tells Don that the same pick-up followed him the night before. He also says that he did not tell him about it because Don was already upset with him for the television interview.
Later, Don discovers there was a pick-up with the same discription seen at the mall where Bonnie went missing.
David accompanies Charlie and Amita to Charlie is put off that he has David following him. Amita is upset that Charlie will not stop working on the case. They exchange a few harsh words in front of an awkward feeling David before she storms out.
Colby and Don are at Bonnie's home. Don tells Colby that he is worried about Charlie, and says "What if...". Colby cuts him off by saying it was not his fault. Don leaves, Colby stays to look around more. He puts in a tape of Bonnie, and appears to become transfixed. He watches more footage, with thoughtful looks on his face.
Back at the University, David is still following Charlie. Larry stops him in the hallway, because he says he wants him to stop working on the case. Ray Ray happens to walk by and sees David with Charlie. He asks about Megan Reeves, he insists she took a liking to him. Larry tells him that he and Megan are involved, and Ray laughs. Larry is insulted, but Ray apologizes and explains he was only laughing because Megan is not the kind of woman who usually went for guys like them.
Back at Eppes home, Don and Alan are discussing Charlie. Don doesn't think he wants Charlie to work with him any more. He feels perhaps he is meant for bigger, better things. Alan tells him that Charlie helping him now could be what he was meant to do, his greatness. Don says that his mom and dad made so many sacrifices for Charlie. And Alan reminds him "We all made those sacrifices for Charlie, especially you."
Back at Bonnie's home, Colby finds utility bills for two different addresses. He calls Don, they suspect the other address is the place where she would keep her confidential work.
The address is a warehouse. When Don and Colby show up, there are a few guys taking boxes of paperwork out. They spot the silver pick-up parked in front. Colby yells "FBI", and then gets shot at. Colby returns fire and hits two of the guys, killing one.
They find more papers with numbers on them, and a picture of the driver of the silver pick-up with a prominent real estate developer, Richard Taylor.
Don bursts into Taylor's office and threatens him to stay away from his family. Taylor seems amused and says he has no idea what he is talking about.
The team finds out that Bonnie had been looking into Taylor's dealings. She figured out that he was forcing residents out for his new project. He was using intimidation and threats.
In Charlie's garage, Colby and Larry are with Charlie while he is unsuccessfully trying to work. Charlie ends up yelling at Larry who was trying to help him. Amita and Ray come in. Ray has brought solar panels for the house. Charlie takes him outside and leaves everyone else in the garage.
David finds out the guy who Colby shot has a brother-in-law who drives a silver pick-up. They track him down and burst into his apartment. There is a guy dead on the couch, the other that Colby wounded earlier at the warehouse, and the driver of the silver pick-up, Sonny Layva. They arrest him.
Outside the Eppes home, Ray is explaining the solar panels to Alan and Charlie. But Colby wants Charlie to get back to work. Overwhelmed, Charlie is nearly in tears and pleads that he can not do it. He is not able to work the math.
At the FBI, Don is interrogating Sonny. Sonny admits that Bonnie is alive, but won't say where unless he has charges dropped.
Don goes back to Taylor's office. He tells him that they have Sonny in custody and it is just a matter fo time before Sonny tells them everything.
Colby takes Charlie to an overlook. He tells Charlie that he felt the same exact way when he was in Afghanistan for the first time. He tells him he has to talk about it, it is the only way to move on. He says no one can hear him. Charlie starts talking about the ordeal. Then he goes back to work.
Charlie works out that the numbers on the papers were properties. Taylor found a way to under value homes, committing real estate fraud. This is what Bonnie Taylor had figured out.
The team figures out there is a house on the list that Taylor actually owns. They believe Bonnie is probably there.
They go there, but there is no one. Colby is distraught. Then he hears banging from the basement.
Colby finds Bonnie tied up, he cuts her loose. She walks out.
Don arrests Taylor.
Eppes home, Ray is telling Alan and Larry that the roof is going to need to be modified for the solar panels. Alan is upset about changing the house. Larry and Ray tell him it was not changing the house, just making it viable for another one hundred years. Alan feels better.
Charlie brings the new pump to the pond with Don's help. Don asks him if he thinks working with him has been holding him back. Charlie scoffs, and plugs in the pump. It works, they go for a beer.