A high school time capsule from 1987 is opened - and contains a teenager's liquefied remains; only the skeleton is intact. Gil Bates, former high school nerd and current assistant manager at Tech Town, tells Booth and Brennan that he sealed the capsule himself, and he doesn't know how the body got in there.
At the lab, the body is found to have several fractures that healed at different times, including a fresh one on the right clavicle. A video shows the 1980s teens loading up the capsule with 80s artifacts. Angela makes a sketch of the victim's face, and Zack realizes he saw the face in the video. The yearbook IDs the awkward young man as Roger Dillon. The remains have traces of a nerve gas; the skeleton's injuries show he had his arm twisted around his back, but some of the fractures on his ribs pre-date high school... so maybe it wasn't bullying.
Booth and Brennan talk to Roger's dad, Daniel Dillon. He never reported his son as missing because his wife told him he ran away. And he's ashamed to say he's not surprised Roger never contacted him again. Daniel used to drink heavily and beat Roger. The last time he saw him, Roger asked for a lot of money, and he threw him out of the house with his arm twisted behind his back. He's stunned to find that Roger's dead, and tells them to talk to Gil, who was Roger's best friend.
Two 80s artifacts are found in the capsule that are not on the list of stuff that went in: an old 5 1/4" floppy computer disk, and a pocket watch that turns out to be filled with cocaine. Both were in Roger's pocket at the time of the murder.
Brennan tells Booth a personal, humiliating story - a boy she was interested in in high school taped a Brainy Smurf to her locker. Booth just sniggers. Brennan's upset, and realizes that Booth was one of "those" guys in high school. Booth has no clue what she's talking about.
Gil is devastated to find that the body is Roger's. He says Roger left a note when he ran away, about not being able to take his dad or the kids at school any more. He says he doesn't know what Roger wanted the money for.
Booth interviews Darwin Banks, who was a young science teacher in 1987, and was arrested in a drug bust just two days after Roger disappeared. He's shocked to hear Roger had drugs on him and is offended that Booth thinks Roger was dealing for him. Banks says he was ratted out not by Roger, but by John Adamson, an arrogant jock who turned him in to the cops when Banks busted him for cheating in class.
Booth asks Dr. Sweets to profile the killer, but he wants to focus on how the partners are doing. He suggests that Booth share a humiliating story with Brennan. His attempts to do so all turn out to actually be tales of victory and sexual prowess.
Further testing shows no trace of cocaine in Roger's body; he didn't do drugs. And there wasn't enough nerve gas to kill him, either. However, the skull shows a tiny fracture that shows a weapon was thrust into the neck; Roger bled to death. Meanwhile, Angela has procured a Commodore Amiga to run the old disk - which contains a 3-D first-person shoot-'em-up game that seems much too advanced for 1987. If this game had come out back then, Roger would have been a billionaire.
Gil is amazed to find that the game exists - Roger used to talk about it; he had no idea he'd actually coded it. They'd been planning to start a gaming business together after graduation; they were working minimum wage jobs to save up the money to buy enough computers to make a 3-D rendering farm - and Roger made extra money tutoring a cheerleader, Janelle, in math... and taking the SATs for jock John Adamson.
Adamson, who is now a political strategist, says Roger tried to blackmail him for an extra $500 after he took his SATs. Adamson gave him everything he had - including his watch. Dr. Sweets, who is running a profile in hopes that helping catch a killer will impress his girlfriend, says if Adamson was the killer, he'd have taken the watch back.
Hodgins finds that the nerve gas is Malathion, which was used to kill mosquitoes in the 1980s. In June of 1987, It was sprayed all over a swamp near the school that was just starting to be developed into a housing area. Roger must have waded right through that swamp. One of the only homes there at the time was the home of Janelle, the cheerleader Roger was tutoring.
The yearbook from the capsule is reconstructed and is found to be a prank version of the yearbook, with captions mocking the popular students, inscribed "Brought to you by Gruff and Grim."
Booth and Brennan interview Janelle, who is now married to high school sweetheart Terry Stinson - a popular guy and former student council VP who is now the school principal. Her memories of Roger are fond; he had a crush on her, and he was sweet. Roger visited her the last day of school to drop off her graded final - probably just an excuse to come see her. Brennan stares at her son, Alex, as he passes through, then sneaks a photo of him out of the house as they leave. Analysis shows he's got no facial features in common with Terry Stinson - but has plenty in common with Roger.
Terry's become a suspect - did he kill Roger for sleeping with his girlfriend? But Terry's genuinely shocked to find that Janelle cheated on him with Roger. Janelle never said anything because she truly wanted to believe that the child was Terry's. She slept with Roger because he made her feel special; back then, Terry was "that guy" - the one who did anything he wanted, and didn't truly need her.
One day, Roger ran to her through the swamp, crying after being beaten by his father, and she wanted to make him feel special too. When she told him she was pregnant, he wanted to marry her. He wanted the money so they could run away together. But by then, she was back with Terry. And Terry was so happy when he heard she was pregnant she knew he wasn't "that guy" any more - that he truly loved her. Terry says that no matter what, he loves her - and Alex is his son. They're a family.
Dr. Sweets says the killer was likely a student, acting rashly. It was somebody who has punished himself for years, and worked way below his potential. And he's been waiting 20 years for the body to be found so he can finally pay for his crime.
The skull fracture and the broken seal on the capsule both contain a tiny stain of liquid petroleum - formerly asphalt - and tinier particles of granite. The murder weapon was an asphalt shovel. And Gil used to pave driveways.
Booth and Brennan interrogate Gil. He was "Gruff" and Roger was "Grim." The night of Roger's disappearance, they went to plant the prank yearbook in the capsule. Booth guesses correctly that Roger asked for his money back that night, for Janelle, ruining their plan of going into business together. Gil had no idea Janelle was pregnant. Roger simply said he loved her. Gil told him that was stupid - she'd never look at him. Roger got angry and hit him, and Gil picked up the shovel and jabbed him with it... and accidentally killed him. Gil is relieved to finally have the story come out, and hopes he can tell Roger's son about his father somebody.
That night at the diner, Booth finally comes up with a humiliation story of his own. His friends were roughing up a geeky kid, dangling him over a stairwell, laughing while he begged and cried. And Booth could have stopped it - but he didn't. He chose sides. Brennan is intrigued, and tells him he's evolved. Slowly. Booth has brought her a Brainy Smurf, and says that Brainy is better than Smurfette, who was shallow and only had her looks. Brennan forgives him, and the two laugh and talk into the night.