During a police training exercise, a State Police Instructor holds a tear-gas launcher and indicates a nearby trailer. This trailer was a mobile meth lab until it was reclaimed three days ago. How was that accomplished? Cadet Williams surmises that the police used tear-gas. He's wrong. It's demonstration time. The State Police Instructor fires a tear-gas grenade into the meth lab. There is a huge explosion, just as he expected. Unexpectedly, a corpse sails through the air and crash-lands on a nearby car windshield. The cadets stare as the corpse burns. Brennan and Sweets wait for Booth in Sweets' office. He is late for their session. When Booth finally arrives, he is elated about the RICO case. This top-secret project is really going to bring in the accolades and, more importantly, a raise. What will he do with that extra money? Spend his birthday in Hawaii, of course. Booth's cell phone rings and he answers despite Sweets' protests. Booth's brother, Jared, is on the phone. Booth makes plans to see him. Sweets wonders why he didn't know Booth had a brother. Brennan knew though she has never met him. After his call with Jared, Booth's phone rings again. So does Brennan's. Their session is cut short as they rush off to look at remains.
At the scene, Brennan examines the corpse on the windshield. The State Police Instructor is beside himself. After learning he was not responsible for the man's death, he leaves to have "a little cry." Brennan realizes that the victim was shot. She pulls a notebook from inside his jacket. It is filled with drawings and designs. "This man was obviously some kind of technical designer or engineer." In other words, he's a Squint.
At the lab, Angela and Hodgins review the victim's sketches. There are plans for an automatic toilet scrubber and a snow shovel with a heating device. The victim was an inventor. They are interrupted by Clark Edison. He has returned to the lab because, although his working style clashes with the other Squints, the Jeffersonian is the best place to get an education. Angela realizes that one of the pages in the book was actually a patent application. The patent application number may help identify the victim.
On the Forensic Platform, Brennan examines the body. She cannot locate an exit wound. "That suggests a .22 or .25 caliber," Cam notes. Clark arrives to report his findings. The X-rays show patterned abrasions on the skull. The victim sustained repeated blows but from what? Booth enters with Jared, his brother. Jared, a Lieutenant Commander in the Navy, has recently been promoted to the head of Strategic Plans and Policy. Brennan notes the resemblance between the brothers. Jared asks Cam to accompany him to a work related cocktail party later that evening. Cam agrees. Angela arrives with the address of the person who filed the patent application. She takes one look at Jared and likes what she sees. "Are you thinking of leaving lesbianism behind?" Brennan wonders. Booth explains to Clark about Angela's new old girlfriend. He isn't interested.
Brennan and Booth sit with Paul and Lily Stegman. Paul filed the patent application. The designs were his. The victim was his father, Jim Stegman. He borrowed Paul's windbreaker and the notebook was in the pocket. Paul hasn't seen his father for three days. In fact, they had only recently reconnected. Jim walked out when Paul was little. "His father wrapped his car around a tree, drunk-driving. Paul was injured and so was his mom." Jim injured himself as well. He had two broken legs from the accident. After he healed enough to use crutches, he left for good. There was an article in a magazine about Paul and his inventions. Jim read it and called his son to reunite. They asked him to stay because he said he was sober. Lily recalls that right before Jim vanished for the second time, he claimed that Mike Campbell, Paul's former business partner, was stealing tools from Paul's workshop. Booth wants to pursue this lead. Booth and Brennan speak with Mike in his garage workshop. Mike wasn't stealing tools from Paul. He was there to talk to Jim. He caught Jim drinking and gambling. He confronted him about it but Jim got physical and told Mike to mind his own business. Mike left it at that. He didn't say anything to Paul because Jim disappeared a few days later. "I figured why should I spoil Paul's last memories of his old man?" Brennan looks through Mike's inventions and comes across one that could have caused the abrasions on Jim's face.
On the way back to the lab, Booth gets a call from Jared. Cam backed out of their date because she is caught up at work. Does Booth know of someone else that could be his date to the party? Brennan volunteers herself.
Brennan walks into the Bone Room to meet with Clark before her date with Jared. She wears a slinky black gown, which Clark doesn't find professional. Clark shows her the X-rays of Jim's bones. "The murder victim was supposed to be a long term heavy drinker yet his bones show no signs of alcoholic osteoporosis." That's not all. Paul reported that his father broke both of his legs. The X-rays show no signs of a break on either leg. The victim is not Jim Stegman.
Brennan sits outside the White House Rose Garden with Jared. She is glad she came. Booth would have been uncomfortable at an event like this. Jared doesn't disagree. "It's like Seeley's afraid of success. He stays in his comfort zone." Jared tells her that he is the opposite of Booth. He doesn't mind taking a risk or being in the spotlight. "Can you give me an example?" asks Brennan. With pleasure. He gives her a kiss.
Cam speaks to Booth while she works at the lab. A DNA match confirms that the victim is Anthony Pongetti, a felon convicted of fraud. Booth wonders why Pongetti would pretend to be Jim Stegman. He also wonders why Brennan hasn't come into work yet. How late were she and Jared out last night? Booth hangs up with Cam as State Police Colonel Ryan Wolchuck knocks on his office door. Wolchuk has a request. "It's extremely embarrassing to the State Police that this homicide victim was blown up during a training exercise." If Booth conceals this detail from the public, Wolchuk would be very grateful, as would many other "movers and shakers." Booth isn't swayed. He refuses to do the favor. Cam confronts Brennan in her office while she works with Clark. "Did you just get in?" Brennan didn't actually sleep last night. Cam decides to give Brennan some advice. Clark curses his bad luck. How is he always caught up in awkward social situations? He retreats when Angela enters and hands him a file. Brennan didn't sleep with Jared. Angela and Cam are relieved but Brennan doesn't understand their reaction. Angela gives it to her straight. "He's Booth's little brother and it would just be a creepy way to have sex with a Booth without having sex with the real Booth." Clark interrupts. After reviewing Angela's paperwork, he realizes she's found the real Jim Stegman. He's in Jeffersonian storage, another John Doe waiting to be identified. Jim Stegman was shot in the heart and then dumped in a river. His body came in last week. Booth and Brennan will have to check out his last known address.
In Bowie, MD, Sheriff Leonard Wilkinson shows Booth and Brennan around Jim's garage apartment. Wilkinson doesn't think Jim Stegman deserved his end. He was trying to clean up his act and stay away from drinking and gambling. Booth and Brennan find no signs of alcohol use but they do find betting slips. One of the slips has Anthony Pongetti's name on it. Wilkinson knows him and he doesn't have anything nice to say. If he wasn't running one scam it was another. Wilkinson asks for more details about what's going on but Booth gets a text from Jared: he's in trouble. He tells Bones they have to go right away.
Hodgins and Clark put the finishing touches on one of Paul's inventions. They've constructed it by looking at his designs. After making a few tweaks, they get it to work. The machine sorts plastic, glass and aluminum into different containers. It also almost sorts a bottle into Brennan's head as she enters. Embarrassed, Clark quickly turns off the machine and gives Brennan the information she needs. The grate found in Mike Campbell's garage did not cause the damage to Pongetti's face. It wasn't hard enough. Had it been used as a weapon, it would have bent. Since it isn't, they need to continue their search.
Jared stands by his totaled car on the side of the highway. Police vehicles flash red and blue. Booth drives up and approaches his brother. Jared says he fell asleep at the wheel. Colonel Wolchuk approaches, having responded to the incident. Booth wants to know what his report will say. Wolchuk is not inclined to do Booth any favors. Jared chimes in. "They get me for DUI, I lose my job, Seeley. I lose my whole career." Booth is ready to play ball with Wolchuk. At the Stegman home, Booth and Brennan tell Lily and Paul about Pongetti. He was the man that was living with them, not Jim. The couple is understandably confused. What's going on? When asked, Lily mentions that Pongetti left a duffle bag in their closet. Brennan pulls it out and begins to go through it. Booth reports that they think Pongetti was impersonating Jim in order to cash in on Paul's inventions. Paul finds that funny. Even he hasn't made money on his inventions. Booth pulls one of Paul's inventions out of the closet. "That's a battery operated electrostatic dust trap." Booth turns it on but it doesn't work so Paul opens it up. There is a brown paper bag inside containing $20,000. "That is the best motive we've seen for murder yet."
In his office, Booth watches a breaking news report. Colonel Ryan Wolchuk makes an announcement about the RICO case that Booth had been working on. "I have the great pleasure of announcing today that the grand jury has handed down 62 indictments following the State Police crack-down on organized crime." Booth grimaces as Wolchuk takes the credit for his investigation. He tears up his tickets to Hawaii and throws away his travel books. Cam pages him.
Booth meets Cam in the autopsy room. She wants to know what happened with the RICO case. Why didn't he get any credit? Booth tries to make up a story about it. It was an order from his superiors. Cam isn't buying it. She knows what happened. Booth tells her to let it go.
Sweets enters the elevator in the FBI building to find Jared. He introduces himself and notices that Jared holds tickets to the Capitals Hockey Team. Sweets still hasn't gotten Booth anything for his birthday but Jared tells him the tickets aren't for Booth's birthday. They are a thank you present. Perhaps they are also an apology present. "Having a big brother is like having an extra dad, only a dad who protects you from your real dad..." Jared muses. He leaves Sweets to ponder this.
In the bone room, Clark and Brennan work with Jim Stegman's bones. Clark has a theory. Whoever killed Jim was trying to torture him for information. Each gunshot wound was exact and calculated. "Middle of the foot, middle of the knee, middle of the shoulder, dead center on the heart." At the FBI, Booth has a new suspect to question. Steve Jackson was involved in a scam with Jim and Pongetti many years ago. However, when they were caught, both Jim and Pongetti ratted Jackson out. He went to jail. Could he have killed for revenge? Booth meets Jackson in the interrogation room. Jackson admits to meeting with Stegman but Stegman was only apologizing as part of his twelve-step program. Jackson doesn't intend for this interview to last very long. He has an alibi. He shows Booth the tracking device on his ankle. "Somebody somewhere knows where I am 24 hours a day since I got out for the next two years."
Booth meets Brennan in the observation room. He tells her that he doesn't think Jackson committed the murders. He is about to leave but Brennan brings up the RICO case. She wants an explanation. "Did you do something wrong?" Booth is offended by her question. Of course, he didn't do anything wrong. She should drop it. He walks away but Brennan isn't done yet. "Jared warned me that you tend to sabotage yourself." Booth gets heated at the mention of Jared. Is she calling him a loser? Brennan deflects but he wants her to answer the question. Booth's phone begins to ring. It's Cam. They found Lily Stegman's fingerprints on the money. Brennan wants to finish their conversation but Booth wants to get back to the job.
Booth and Brennan question Lily Stegman in Booth's office. She didn't murder Jim but she did know about the money. It arrived in a package addressed to Jim. When he never came back, Lily opened it. The money was inside and there was also a note. "Jim, Do me a big favor. Hold on to this until I can get it back from you. Help yourself to whatever you need. P." Lily is ashamed she didn't say anything sooner but her family needs the money. She is the one who hid it inside Paul's invention. She also hid the rest of it, putting $150,000 in their safety deposit box.
As they drive, Booth gives his theory to Brennan. Pongetti came into some money, illegally. He sends the money to Jim Stegman at his son's home to keep it hidden. However, Jim Stegman is murdered. That means in order for Pongetti to get his money, he has to go to Lily and Paul and pretend to be Jim.
Cam and Sweets call Brennan into the lab. They are worried about what's going on between Booth and Jared. Due to their abusive family life, "Booth's been digging Jared out of trouble since they were kids." Sweets agrees this is not healthy. Jared has had no opportunity to face the consequences of his actions. Brennan doesn't believe them. There's no proof. Cam goes on to say that she knows Booth lost the credit on the RICO case because of Jared. Again, Brennan needs evidence. They ask Brennan to give Booth the benefit of the doubt but all she can focus on is evidence. Cam tells her that Jim Stegman and Pongetti were killed with the same gun. There's some evidence. They were most likely killed by the same person. Brennan meets Jared at the Founding Fathers Bar. She asks him if he knows why Booth lost credit on the RICO case. Jared hasn't heard anything about it but when Brennan mentions that the State Police received the credit, it becomes clear. Jared asks Brennan to leave this "between brothers." Brennan is suddenly overcome with anger. "You took advantage of him. You know, you made me think that he's a loser. And what really makes me angry is that I believed you. You know, I wouldn't blame Booth if he never spoke to me again. You're the loser." Before she storms off, she pushes him off his chair.
Booth drives as Brennan listens. The cash was recovered from Lily Stegman's safety deposit box. It was wrapped in evidence bands. "The money is from the county sheriff's headquarters in Bowie. It was confiscated during a drug bust." The money had been scheduled for transport but a fake driver showed up claiming it. Booth thinks that Pongetti posed as the driver. Brennan wonders why no one recognized him. After all, Sheriff Wilkinson said Pongetti had been in custody two months ago. Booth realizes Wilkinson must have posed as the driver. He turns the car around. The Stegmans are in danger.
At the Stegman home, Lily explains to Sheriff Wilkinson that they gave all the money to the FBI. As he exits their home, Booth stops him. Brennan examines Wilkinson's car. She realizes that the grating in the police vehicle matches the cuts on Pongetti's face. Wilkinson sped up and slammed on the brakes, sending Pongetti's face into the barrier between the back and front seats. Wilkinson feels cornered. He grabs Lily Stegman to use as a hostage. Paul tries to save her but Wilkinson hits him with the butt of his gun. Bones convinces Booth that if they switch guns, he could get a shot at Wilkinson. This causes Wilkinson to shoot Brennan. Booth is distracted and Wilkinson drags Lily into his car. He drives away and then pushes her out. Booth begins to fire, one bullet after the other, until Wilkinson crashes his car. Brennan and Lily are both fine but Wilkinson is dead.
At the Founding Father's Bar, everyone is gathered to celebrate Booth's birthday. Brennan makes a toast, her arm wrapped in a sling. "Anthropology teaches us that the alpha male is the man wearing the crown, displaying the most colorful plumage and the shiniest baubles. He stands out from the others. But I now think that anthropology may have it wrong. In working with Booth, I've come to realize that the quiet man, the invisible man, the man who is always there for friends and family, that's the real alpha male." After the toast, Brennan pulls Booth aside. She tells him to stop covering for Jared. It's time to let go. Jared needs to learn to help himself. Booth confesses that he got Jared off the hook for drunk driving by giving the RICO investigation to the State Police. Booth thinks she should understand. She helped her father get off for murder. The only difference is that Brennan's father will never commit murder again. Booth needs to talk to Jared.
Booth brings Jared outside. He asks him to stop drinking. Jared laughs it off as a joke but Booth is serious. He has to stop protecting him. Still, Jared brushes him off. He downs his drink and goes back inside. Booth's anger bubbles up. He punches a bus stop shelter. Brennan comes outside with cake. She sits next to Booth at the bus stop and gives him a fork. Booth tells her that his dad drank. They sit in silence.