Bones: The Best Episode In Every Season, Ranked

Dr. Temperance “Bones” Brennan and FBI Agent Seeley Booth solve crimes while dancing around each other in an ongoing will-they-won’t-they love affair that left fans on the edge of their seats for several seasons. For 12 seasons, Bones was an amazing criminal investigation show that shook up the normal procedural stereotypes by making Bones a closed off woman and Booth a rebellious and fun-loving agent. Based on the book series by Kathy Reichs, based on her own life, the show was nominated for two Emmys and won several others. Here are the best episodes from every season, ranked.

12 Season 9: The Recluse in the Recliner

Agent Seeley Booth is prepping for a congressional committee hearing to screen him for a job in the FBI Berlin office, which is supposed to be a formality. He continues to oversee a murder case of someone who had offered Booth information about a supposed government cover-up. But as they continue to investigate, it becomes clear that this is going deeper than they could have guessed, and Booth might just be over his head. 

In the end, the FBI turns on Booth and he is sent to jail, leaving the future of his family up in the air. It was one of the biggest cliffhangers in the show’s history.

11 Season 7: The Past in the Present

A long arc of chasing serial killer Christopher Pelant culminates in this episode that kept viewers on the edge of their seat. The computer genius is trying to ensure that he wins his criminal trial by discrediting the Jeffersonian team. In a series of moves that get members of the team dismissed as a witness of suspended from duty, Pelant manages to manipulate everyone until he’s released. Worse, it looks like Bones committed murder, and they know that Pelant must have somehow framed her, even though he’s on a short leash. 

In the end, Bones must go on the run or risk going to jail for one of Pelant’s crimes.

10 Season 10: The Conspiracy in the Corpse

This season premiere was one of the most heartbreaking episodes in Bones history. After the team realizes that Agent Seeley Booth was framed by the FBI of killing three innocent agents, Dr. Brennan works to free him from jail. She even goes behind his back and blackmails the prosecutor. Booth is able to come home, just in time to learn Sweets and Daisy are having a baby. 

But things go terribly wrong: In the course of an investigation, they realize the conspiracy runs deeper than seems possible. Sweets is killed by someone who manages to steal the evidence that Sweets had collected against him.

9 Season 6: The Hole in the Heart

This is one of the few episodes that opens up without an extant murder case for the team at the Jeffersonian to solve. Instead, Dr. Hodgins is helping Nigel prepare a mechanical demonstrating that compares human versus tyrannosaurus rex in a fight for a paleontology conference. 

Agent Booth is told that a sharpshooter, Jacob ‘Jake’ Broadsky, that Booth has tracked in the past has killed again. Broadsky is targeting ‘traitors,’ such as Booth and the whole Jeffersonian team. They try to figure out how the killer is targeting his victims, and Booth accidentally hands Nigel the cell phone that Broadsky is using, which ends in Nigel’s death.

8 Season 11: The Nightmare in the Nightmare

The Jeffersonian team has to search for The Puppeteer, a serial killer who they’ve dealt with in the past. He’s known for living with his victims’ bodies before disposing of them. Brennan has to work through her guilt over retiring, because it prevented her from stopping him earlier. 

In fact, Brennan sees her therapist, Dr. Faulk, to deal with a series of nightmares she’s been having about a burned figure wandering around a dark lab. Little does she know that her nightmares will soon become reality when she’s kidnapped by a familiar face who wants to help her find the murderer.

7 Season 5: The Parts in the Sum of the Whole

In the milestone 100th episode, Dr. Brennan and Agent Booth help Dr. Sweets finish his book about their partnership by telling him about their very first case together. We’re taken through flashbacks that reveal how their entangled romantic beginnings almost doomed the partnership from the start.

Booth had been brought on to a case by a mother desperate to know who murdered her daughter. Camille, who was then a coroner, suggested that Booth consult the Jeffersonian expert, Bones, who might be able to help him learn more about the crime by studying the bones. He had his doubts, but Booth comes away from the case impressed by Brennan and her team, setting the groundwork for a very successful partnership.

6 Season 12: The Day in the Life

This penultimate episode of Bones sets in motion the last storylines every character has. Importantly, it brings closure to the storyline of Zack Addy, Dr. Brennan’s apprentice-turned-murderer who was locked away in season three for helping a serial killer, Gormogon, commit his crimes. In this episode, Brennan testified for Zack, ensuring that his appeal resulted in an exoneration. It was a good ending to a long and sad story. 

Meanwhile, Angela reveals some big news, and Mark Kovac escapes from prison, sending Agent Seeley Booth on a race to protect himself and his loved ones from Kovac’s most dangerous revenge plan yet. 

5 Season 4: The Hero in the Hold

Dr. Jack Hodgins, Dr. Brennan, and author Thomas Vega are officially suspected of stealing FBI evidence relating to a serial killer known as the Gravedigger. To get what he wants back, the Gravedigger kidnaps Booth and threatens to let him suffocate him in a coffin within 24 hours unless the evidence in paid as ransom. Hodgins admits he has it, but wants to try to find Booth without giving up the evidence first.

Locked in the coffin, Booth hallucinates about Corporal Edward ‘Teddy’ Parker, who he failed to save in combat. Meanwhile, Booth’s brother Jared shows up to risk everything in order to get his brother back.

4 Season 3: The Wannabe in the Weeds

The corpse of Tommy Sour is found in a field, horribly mangled by a harvest shredder. He was a fitness instructor in a gym and an amateur singer in a nightclub; he made a lot of enemies in both places. He was also being stalked by a gym client, who Dr. Sweets evaluates and believes is absolutely capable of murder. Unfortunately, her obsession suddenly turns toward Agent Booth, with bad consequences. The team searches for the killer seemingly fruitlessly, until something strange convinces them to look in the right places. The episode is great because we see Zack and Brennan sing, as well as strong evidence of Booth’s real feelings for his partner.

3 Season 8: The Patriot in Purgatory

Brennan brings the group of interns together to try to get them to work as one team. She assigns them the task of identifying as many of the unsolved cases as they can, and while most of them focus on numbers, Arastoo focuses on solving a particularly difficult one. As the team digs deeper, they discover that he may have been involved in 9/11 somehow—but was he an attacker or a victim? 

The solution is a heart wrenching story about a veteran who saved lives but struggled to adapt to civilian life. Booth honors him beautifully, and the episode didn’t leave viewers with a single dry eye. 

2 Season 2: Aliens in a Spaceship

A report of “two aliens” in a large vat ends up being the gruesome grave of two twin (human) boys, who had been missing for years. It’s again the work of a serial killer known as the Gravedigger, who kidnaps and buries his victims before asking for a huge ransom.

But the Gravedigger is another step ahead of them. He kidnaps Bones and Hodgins from the Jeffersonian parking lot, and asks for a ransom of $8 million. They aren’t found within the time allotted, but use enough tricks to save and make oxygen to survive until Booth is able to rescue them. Booth and Brennan share a moment at the end that really ratcheted up the sexual tension and the will-they-won’t-they debate. 

1 Season 1: The Man in the Fallout Shelter

Angela wants to celebrate Christmas, and Agent Booth’s version of a Christmas present is to give Bones a 50-year-old corpse. However, when they cut into the bones, they release a mold that causes a life-threatening disease. Everyone is quarantined in the lab until they can be sure they’re not infectious. 

The team finally learns about each other, including that Agent Booth has a son and that Dr. Brennan’s parents disappeared on Christmas Eve. They still manage to exchange handmade gifts Angela made. It’s a sweet episode, and one of the first episodes that made the show more than just its procedural roots. 

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