At the FBI, BRENNAN, HODGINS and Grave Digger author THOMAS VEGA face JUDGE DIX WILLIAMS and AUSA HEATHER TAFFET. This is not a social call. Taffet was recently assigned to "The Grave Digger" case after AUSA Kim Kurland died in a car accident. Subsequently, Taffet realized that not all evidence from the investigation was in her files. She accuses Hodgins, Brennan and Vega of stealing the missing evidence. The judge orders the culprit to turn it over to Taffet by the end of the day.
In Booth's apartment, BOOTH meticulously adjusts his "Cocky" belt buckle. As he admires his tux, the phone rings. It's Brennan. She's worried that Booth will be late to her award ceremony (she's being honored for her scientific achievements). Booth lies and tells her he is on his way. She catches on to his ruse when he hangs up to answer a knock at his door.
Brennan, clad in a gorgeous gown, rushes into the Jeffersonian to find SWEETS, CAM and ANGELA waiting for her. They're all dressed for the ceremony as well. As they head out of the lab, Brennan's phone rings. She hears a distorted voice on the other end. "I have taken Seeley Booth. He has been buried alive. He has 21 hours to live. Bring the evidence to the SW5 DC boundary stone in return for which you will receive GPS coordinates. If you involve law enforcement, I will know and Seeley Booth will die. This is my final communication."
Booth wakes up disoriented but he manages to turn on the tiny light on his watch. He is trapped inside of something. He bangs on his cage, struggling to free himself.
Meanwhile, Cam, Brennan, Sweets and Angela search Booth's apartment. They discover that Booth was dragged through his window. Angela wants to call the police but Sweets knows they have to pay the ransom. Brennan doesn't have the evidence the Grave Digger wants. Angela gets on her phone. Hodgins was accused of stealing the evidence too. He could know something.
Booth continues his mission to free himself. He locates his car keys and uses them to loosen a bolt above his head. It takes all of his strength but the bolt comes off. Booth kicks the rest of the bolt upward and sees a sliver of light.
An adrenaline pumped Hodgins meets Brennan at the lab. He is ready for this case. How much time do they have? Brennan does not share his enthusiasm. She demands that he turn over the evidence he has to her. Immediately.
Booth loosens another bolt. He pushes and the metal hatch opens. Booth sticks his head through the hatch and finds himself in a large room. He tumbles out of his prison and realizes it's nothing more than a yellow submarine, something a child might play in. Booth paces, surveying his surroundings. He's not alone. CORPORAL TEDDY PARKER emerges from the shadows. Booth believes he's hallucinating because Teddy is an army buddy who died years ago.
At the lab, Hodgins shows Brennan a metal case. It contains a multitude of evidence as well as the one thing the Grave Digger wants: a piece from the bumper of the Grave Digger's vehicle. Booth has 19 hours left. Hodgins wants the team to use 10 of those hours to identify the Grave Digger. Brennan decides they can use 8 of the hours to conduct an investigation. After that, they save Booth.
In Angela's office, Angela and Brennan analyze the recording Brennan made of the Grave Digger's call. The voice is unidentifiable but Angela compares it with the call from Brennan and Hodgins' kidnapping. The same person made both calls. The only other thing Angela can gather is background noise. Brennan and Angela listen to it again and again. They hear waves and seagulls. The Grave Digger was near the water.
Booth uses a propeller from the submarine to chip away at a door in the wall. Teddy brings him a new propeller when the first one bends. Booth takes it and keeps at the panel until water sprays through from the other side. Uh-oh. The spray gets heavier. Water gushes into every crevice.
At the lab, Angela plays the recording of the seagulls for Cam and Hodgins. Cam hears something else: a merry-go-round. The Grave Digger was at King's Beach Boardwalk. Hodgins makes the connection: Vega lives just off the boardwalk.
Brennan and Hodgins walk through Vega's parking garage. As they prepare to confront him, Brennan notices Vega's car. Someone is inside. They slowly approach to find Vega dead in the front seat. Hodgins and Brennan wonder if they should take his body to the lab but they are interrupted by AGENT PAYTON PEROTTA. She tells them to step away from the car.
Booth and Teddy try to stay afloat as more water fills the room. Booth sees a door above their heads. They'll be able to reach it once the water level rises.
In the parking garage, Perotta questions Brennan and Hodgins. They tell Perotta they were meeting Vega for a book interview when they found him dead. Perotta admits she was following the pair, as they are under suspicion of stealing evidence. Thinking fast, Brennan suggests that Vega was in possession of the desired evidence. That's why he was killed. Perotta lets Hodgins and Brennan leave but they will hear from her again.
Booth and Teddy pull themselves out of the water onto the ledge leading to the door. Booth prepares to struggle with another door. Teddy hopes they find something better behind door number two than they did behind door number one.
As they drive, Hodgins calls Angela at the lab to tell her that Vega is dead. Their situation just became precarious: Hodgins and Brennan spoke to the FBI. That was against the Grave Digger's rules. They have to turn over the evidence now or they are risking Booth's life.
As the water bubbles around Booth's ankles, Teddy emerges from the water with the periscope from the submarine. He gives it to Booth, who shoves it into the door's wheel. They both use it to turn the wheel and unlock the door. Booth and Teddy barrel through the door before the water can follow.
Teddy and Booth find themselves in a room filled with plastic sea creatures. They come to a locked gate. Teddy begins to pick the lock with one of Booth's cufflinks. Booth watches, thinking about the fact that Teddy was just a kid when he died. Twenty years old. Teddy asks if Booth has children. Booth tells him about Parker. Teddy is touched, realizing that Booth named his son after Teddy. Booth finds another hatch. It's a porthole. Booth sees open water: they are on a ship. Teddy notices something else: this particular ship is rigged with explosives.
Brennan drives to the boundary stone with Sweets, Angela and Hodgins. When they arrive at the drop site, Angela detects a video signal with her computer. The Grave Digger is watching. Angela hacks into the signal as Hodgins and Brennan approach with the evidence. The camera zooms in, ensuring everything is there. Angela realizes that the Grave Digger is very close. Sweets notices a frequency change on the computer. Brennan and Hodgins are in danger. Angela yells to them and they start to run, not making it far before the boundary stone explodes. Perotta arrives, demanding an explanation.
At the FBI, Perotta brings the squints in front of Judge Dix Williams and AUSA Taffet. They refuse to speak so Perotta reports that Grave Digger evidence was destroyed in the explosion. Judge Williams is not amused. The squints will no longer be allowed access to anything involving the Grave Digger.
On the ship, Teddy explains that the ship is being sunk to form a reef for fish. School children decorated it. Booth finds the transponder. They have less than seven hours before the explosion. Booth knows they can use the transponder to send a signal. Teddy knows that if Booth disconnects the transponder, nothing can stop the explosion. Booth decides to risk it.
As the squints leave the FBI, Brennan wonders why the Grave Digger hasn't sent Booth's coordinates. Sweets gives the hard truth: the Grave Digger may have no intention of releasing Booth. He obliterated the evidence against him. Maybe he's "cleaning up." Maybe Brennan and Hodgins were meant to die in that explosion. Brennan will not give up. There is one more person she can ask for help.
Brennan meets JARED BOOTH at the Founding Fathers Bar. She tells him the situation and asks him to get her Vega's remains. Jared is taken aback at the request. He decides to make a few phone calls. Brennan tells him it isn't that kind of situation. His lack of concern makes her angry. She storms out, telling Jared that he never deserved Booth.
On the ship, Teddy and Booth work to feed the transponder signal through the ship's antenna. Booth takes this chance to apologize to Teddy. Teddy is haunting him because of the last mission. Teddy never should have gone on that mission. Teddy responds that he is simply there to help. Booth is ready with the transponder. He turns it on and it seems to work but after a moment, it shorts out. Now they are really in trouble.
At the lab, Jared arrives with Thomas Vega's remains. Brennan and Cam meet him at the door. Brennan thanks him, hoping they can get the clues they need to rescue Booth.
Booth searches the ship for a way out while Teddy follows with a flashlight. He runs through their options: death by explosion, drowning or hypothermia. If Booth dies, no one will be left to remember Teddy. Booth mentions Claire. Claire will remember. She puts flowers on his grave every year. Booth never speaks to her because she blames him for Teddy's death. Booth blames himself, too. Tomorrow is the anniversary of Teddy's death. If Booth survives, will he tell Claire that Teddy loved her? Booth notices a wall with a bolt pattern, indicating stairs. They are going to blast their way into the stairwell.
At the lab, Jared explains that he brought the remains here under the guise of a military intelligence operation. When the ruse is discovered, he'll lose his job. Brennan notices fractures on the victim's X-rays. He fought back. The Grave Digger should have injuries, broken ribs at the least.
On the ship, Booth uses the available explosives to rig the wall to blow. Teddy arrives with a charge. All they need now is a power source. Teddy decides he can part with his flashlight.
At the lab, AUSA Taffet arrives to reclaim Vega's remains. She shows them the warrant and Brennan notices something strange. She can't extend her arm. Brennan pushes on her ribs and Taffet recoils in pain. Hodgins believes she could indeed be the Grave Digger. Jared suggests they lock her up.
In the Jeffersonian locker room, the team surrounds Taffet. She won't talk so Hodgins suggests "spring cleaning." Jared denies the existence of these top-secret government files...at first. After a moment, he decides to get Taffet's file. Cam leads him to a computer.
On the ship, Booth prepares to set off the explosion. He needs to complete the circuit while still being far enough away so as to not be injured. Teddy runs for cover.
At the lab, the squints wait with Taffet. They contemplate killing her but Jared returns. From her file, he discovered that she was married for one month to a man named William Burton. She used the marriage to create another identity. With that identity, she rents a storage locker in Spring Hill. Jared sends agents to inspect the locker. They find a van, a stun-gun, boots and a hazmat suit.On the ship, Booth pushes the belt buckle toward the leads to complete the circuit. Teddy worries that Booth is too close. He'll be hurt. Teddy walks to the leads and picks up the belt buckle. Booth chases after him. Teddy slides the buckle across the floor. It touches the leads, completing the circuit. There is a huge explosion. Teddy and Booth both go down.
At the lab, the squints have no luck reasoning with Taffet. The items from her storage locker arrive and the team rushes to work, analyzing the new clues.
On the ship, Booth stirs after the explosion. He can't see very well but he finds his way to Teddy. Teddy is bleeding. This seems to be a repeat of the day Teddy died. Booth asks Teddy to be his eyes. He will support Teddy as they escape: together. Teddy tells Booth to steer them toward the light.
At the lab, Hodgins finds marsh mosquito and paint chips on Taffet's boots. He rushes off to analyze the paint while Angela looks over Taffet's government file.
Meanwhile, Booth and Teddy make progress up the stairwell. Teddy stops Booth for a moment. He doesn't want Booth to blame himself for his death. It wasn't his fault. Booth told Teddy to take cover but Teddy didn't listen. Booth continues to haul Teddy up the stairs.
At the lab, Hodgins has the results from the paint. Taffet was on an old Navy vessel within the last 24 hours. According to the file Angela is reading, Taffet volunteered at the aquarium. They were prepping a ship to be sunk to make a reef. Jared gets on his phone as Angela tells Brennan the news. Before Brennan leaves to rescue her partner, she smacks Taffet with a briefcase.
Brennan flies toward the ship on a helicopter. Jared has been arrested by the Navy and has to give her the low down via cell phone. They couldn't stop the explosion because something was wrong with the transponder so Brennan will have five minutes to locate Booth. Brennan is panicked. That isn't enough time. Unfortunately, it's all they have before the explosion.
Teddy and Booth emerge onto the deck. Booth sees the helicopter hovering overhead. The helicopter lands and Brennan calls to him. Booth turns back for Teddy but no one is there. He hesitates, not wanting to leave without him, but Brennan's screams send him running. He makes it to the helicopter. They take off as the ship explodes. Brennan embraces Booth and isn't letting go anytime soon.
At Arlington National Cemetery, Booth thanks Brennan for saving his life. She presents him with a new "Cocky" belt buckle, much to his delight. He tells her about Teddy. Brennan comes up with a host of reasons for his hallucination but Booth is sure Teddy was real. He tells her Teddy is buried in this cemetery and he is about to deliver a message for him. Booth spots Claire and walks over to her. They embrace. As Brennan watches this, Teddy walks by her. Without Brennan realizing who he is, the two exchange pleasantries. Teddy waves to Booth and Booth waves back. Brennan thinks that Booth is waving to her so she waves. Claire places the flowers on Teddy's grave.