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'Bones' Says Goodbye After 12 Seasons: A Look Back at Brennan and Booth's 22 Best Episodes

by Meredith B. Kile 5:50 PM PDT, March 27, 2017
Photo: FOX

Bones signs off on Tuesday, after 12 seasons of crime solving, evidence examining, blood, guts and, most importantly, bones. But at the core of the long-running Fox procedural -- the “heart of the matter,” if you will -- was a partnership between forensic anthropologist Temperance Brennan (Emily Deschanel) and FBI Special Agent Seeley Booth (David Boreanaz).

From their first episode together, Brennan and Booth’s dynamic was electric, and while the will-they-or-won’t-they of it all took nearly seven seasons to sort out (more if you count that they don’t actually tie the knot until season nine), their relationship kept fans hooked for all 245 episodes. We watched Brennan wrestle with her feelings as Booth looked for love, saw them lay it all on the line only to yank it back again, and finally, at long last, got to witness their happy ending. Two kids and countless hurdles later, they’re still going strong.

So, as we say goodbye to Booth and Brennan -- and the rest of the beloved “Squint Squad” -- here’s a look back at some of the pair’s very best hours together:

22. “The Loyalty in the Lie/The Brother in the Basement” (Season 11, Episodes 1 & 2)

The show’s 10th season finale, “The Next in the Last,” was written before producers knew whether or not they’d be coming back for an 11th year -- and featured Booth and Brennan stepping away from the crime-solving life as they prepared to welcome their second child. So in the two-part season 11 opener, Bones was tasked with bringing back its core twosome in a believable yet suspenseful way, and they went right for the gut.

When charred remains turn up at the Jeffersonian, all signs point to them being Booth’s. Unsurprisingly, Brennan refuses to accept it, throwing herself back into the work and mentally cataloguing every injury her husband sustained throughout his traumatic childhood and heroic adult life in the hopes of finding something to refute a mountain of physical evidence. As she eventually discovers, Booth is alive, and the similarities in the skeletal structure point her to the real victim: his younger brother, Jared (Brendan Fehr). The elder Booth is merely off trying to be the hero again, a shot in the gut his only reward for trying in vain to save state secrets and his brother’s life.

Photo: FOX

Thankfully, Brennan gets to him in time once again, and the two-parter closes on a hospital room scene that calls all the way back to the pair’s season one dynamic. They recover, reconnect and discuss returning to their respective jobs, admitting their undying love for the work that brought them together in the first place.

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21. “The Secret in the Siege” (Season 8, Episode 24)

The eighth season finale was an emotional roller coaster for the couple, riding out both the joy of Brennan’s spontaneous proposal and the tense heartbreak when Booth pulls a 180 and says no after being threatened by super-hacker big bad Christopher Pelant (Andrew Leeds). While the final scenes are hard to watch, the episode is a can’t-miss, thanks to Brennan’s speech to Booth when she asks him to marry her, which is somehow even sweeter than the moment she tells him, “You are not allowed to die. Do you understand?”

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Bonus points to the ensuing scene where Brennan adorably tells Cam (Tamara Taylor) and Angela (Michaela Conlin) about the engagement, before immediately moving on to the link she found between the murder victims. Classic Bones.

20. “The Pain in the Heart” (Season 3, Episode 15)

Perhaps another controversial pick due to fans’ mixed feelings about the reveal that Brennan’s assistant, Zach (Eric Millegan), was big bad Gormogon’s apprentice in the show’s season three ender, which aired following the 2007-08 Writers Guild strike. However, the finale is a big one for Booth and Brennan, who deal with serious emotional fallout after the FBI agent fakes his own death to go undercover and his partner is not informed -- beer hats in bathtubs, anyone?

The episode -- and therefore, the season -- ends with Booth assuaging Brennan’s feelings of hurt and guilt at Zach’s betrayal in a sweet personal moment that’s a preview of things to come. As the team at the Jeffersonian look through Zach’s favorite stuff and Brennan worries that she never gave her former assistant anything tangible, Booth finds the acceptance letter she sent him three years ago and reads it aloud. “I think you gave him something great, Bones.”

Photo: FOX

19. “The Crack in the Code” (Season 7, Episode 6)

The more obvious choice would probably be the episode following this one, “The Prisoner in the Pipe,” when Brennan gives birth to the couple’s daughter, Christine, but watching Booth finally find his family’s home is just too endearing.

Photo: FOX

After wrestling with his feelings about income disparity, the FBI agent goes out on a limb, buying a dilapidated house at a police auction. It’s a gamble, but it pays off, and Brennan absolutely loves the place. She can “see its bones!” It’s too much, really. Plus, these two living in a house that was the site of a U.S. Marshal raid is so very appropriate (and a truly unfortunate case of foreshadowing).

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18. “The 200th in the 10th” (Season 10, Episode 10)

After flashing back to the start of Booth and Brennan's relationship for the 100th episode, Bones celebrated the even more elusive 200th by rewinding further, casting the couple -- and their merry Squint Squad too, with hilariously perfect results -- in an Alfred Hitchcock-inspired murder mystery.

Photo: FOX

Watching Brennan and Booth -- cast this time around as a young LAPD detective and a jewel thief with a heart of gold, respectively -- play cat and mouse all over again in the stylized glamour of a 1950s Hollywood production was the perfect tribute to the show, the cast and the central couple that was its heart for 200+ episodes.

17. “The Beginning in the End” (Season 5, Episode 22)

Following an emotionally fraught season -- which saw the Jeffersonian team through the harrowing Grave Digger trial and Booth and Brennan’s relationship through a failed attempt at laying it all on the line -- everybody’s hearts broke just a little more when the partners decided to “take a break” in the season five finale, throwing themselves back into their relative fields of expertise.

After one last metaphor-heavy case, about a hoarder who died because he couldn’t let go of the past and love what was right in front of him, watching Brennan flee to the Maluku Islands and Booth ship off for a training mission in Afghanistan is gut-wrenching in itself, until he shows up at the airport to say goodbye. May today’s binge-watchers never know the anguish of watching those two not kiss before jetting off to opposite corners of the world, and then having to wait months to find out what happened next. (Spoiler alert: Her name is Hannah and she’s very nice, but no thank you.)

Photo: FOX

16. "The Woman in the Sand" (Season 2, Episode 8)

Booth and Brennan’s first undercover episode -- as boisterous blue-collar Vegas tourists Tony and Roxie -- is rife with TV tropes, but it’s still one of their best, letting the pair turn their chemistry up a notch as they play at wise-cracking sweethearts while trying to piece together the murder of an underground fighter.

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From Deschanel-as-Brennan’s pitch-perfect Roxie character, to her brash recklessness while confronting the Vegas mob, to the sweet and ingenious revelation that she used her beginner’s luck to bet on Booth’s Fight Club-style brawl -- not to mention all of Booth’s double takes at his fake almost-fiancee’s transformation -- this one will always be a winner.

15. “The Foot in the Foreclosure” (Season 5, Episode 8)

A bright emotional spot in the otherwise heavy season five was the introduction of the late Ralph Waite as Booth’s grandfather, Hank, aka “Pops,” who shows up to provide some insight to Booth’s troubled past and -- after becoming the umpteeth person to see that his grandson and his “bone doctor” belong together -- help nudge the pair just a little closer.

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Pops tags along as the partners solve the mystery of a pile of ashes found in a foreclosed house, and later, confides in Brennan that he was responsible for sending Booth’s abusive father away after he found out the man was beating his sons. “When the time is right, you’ll tell him,” the heartbroken grandfather persuades her. “And if he needs it, you’ll hold him?”

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14. “The Man in the Morgue” (Season 1, Episode 19)

As Michelle Hurd’s local New Orleans detective, Rose Harding, deadpans to Brennan after Booth muscles his way into her hospital room, “Guy flies down from D.C., you’re more than just sort of.” Everyone knew it, even back in season one!

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Booth rushing to Brennan’s side and defense when she becomes a suspect herself -- and finding her mother’s earring at the crime scene -- isn’t even the half of it, though. The biggest, most romantic moment of this whole episode might be the introduction of fan favorite Caroline Julian (Patricia Belcher), who will end up becoming perhaps the biggest Booth and Brennan shipper of all. Hello, Cherie!

13. “The Verdict in the Story” (Season 3, Episode 13)

Brennan’s two families come head-to-head during the trial of her father, Max Keenan (Ryan O’Neal), as every other member of the Jeffersonian team is called as expert witnesses for the prosecution. However, the anthropologist plays it cool, insisting she’s fine to her co-workers, FBI psychologist Sweets (John Francis Daley), and even Booth as they all prepare to take the stand in support of evidence that Max killed the deputy director of the FBI.

Photo: FOX

Everything goes according to plan until Booth realizes that Brennan’s plan to prove her father’s innocence involves implicating herself in the murder instead, something he’s unwilling to go along with, even under oath. After 12 seasons, it’s difficult to pick a seminal line for these two, but “That’s a lot of heart, Bones” is certainly in the top five.

12. “The Blackout in the Blizzard” (Season 6, Episode 16)

The “will they or won’t they” couple’s final push towards “they will” wouldn’t have been complete without a classic “stuck-in-an-elevator” episode, and Bones’ comes with the added bonus of having the elevator be an old-school, open-air wrought-iron model, so Sweets can pop by from time to time and update Booth and Brennan on the case-of-the-week while also prying into their personal conversations.

Photo: FOX

This wintry episode does mark a turning point, however. After agreeing to the psychologist’s suggestion that they finally talk about their relationship, Brennan goes as far out on the limb as she’s been since getting shot down earlier in the season, positing that “a time could come when you aren’t angry anymore and I’m strong enough to risk losing the last of my imperviousness. Maybe then we could try to be together.” Booth suggests they each write down a date, before burning the slip of paper to release the wish into the universe. Something good is right around the corner.

11. “Mayhem on a Cross” (Season 4, Episode 21)

Whenever Booth’s old friend, psychologist-turned-chef Gordon Gordon Wyatt (Stephen Fry), is in town, it’s a good time for all. That rule holds true for this season four episode that starts out in the world of Norwegian black metal and ends on a heartbreaker, with Booth and Brennan sharing some of their darkest childhood secrets with Sweets in order to “metaphorically compare scars” with the young FBI shrink, who has a similarly mottled past.

Photo: FOX

The charged moment -- Booth makes his confession only at Brennan’s insistence, then asks if she’s OK -- is for Sweets’ benefit, but it’s also an unmistakable step in the couple’s now-undeniable emotional relationship. Plus, the final moments of the episode reveal the telling title of the psychologist’s book about the pair: Bones - The Heart of the Matter.

10. “The Hero in the Hold” (Season 4, Episode 14)

Booth’s Grave Digger episode features some stellar acting from Boreanaz as well as Shameless star Noel Fisher, who plays Teddy Parker, a young corporal who served with Booth in the Army and tragically became his son’s namesake after dying in combat. Parker shows up on the doomed Navy ship that Booth is held captive on, but he can’t be much help because he’s a ghost -- or can he?

As Booth wrestles with his imaginary demons, as well as the very real danger of his kidnapping, it’s Brennan’s turn to bust skulls on the outside, calling in favors and wrangling Booth’s brother, Jared, to help find him before time runs out. When they do -- in the nick of time, as always -- she accompanies him to Arlington to pass along a message from Teddy to the woman he loved, in a scene that proves Brennan’s faith in Booth is unshakeable in more ways than one.

Photo: FOX

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9. “The End in the End” (Season 12, Episode 12)

Details TBA to avoid spoilers, but just trust us on this one.

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8. “Two Bodies in the Lab” (Season 1, Episode 15)

This season one thriller is not only one of the first, great instances of the pair risking their lives to save each other -- Booth goes into full hero mode, busting himself out of the hospital to rescue Brennan from an undercover FBI agent-turned-killer (played by Adam Baldwin) -- it’s also the introduction of Foreigner’s “Hot Blooded,” which the pair dance to in Brennan’s apartment before Booth gets blown up by a bomb in the refrigerator.

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Despite this, or perhaps because of it, “Hot Blooded” would hilariously and inevitably become the couple’s song, making several more appearances in later seasons.

7. “The Woman in White” (Season 9, Episode 6)

As expected, Booth and Brennan’s wedding was anything but conventional, but it was perfectly them. From the squinterns showing up in old-timey costumes from various Jeffersonian exhibits to Booth’s Army chaplain, Aldo (Mather Zickel), marrying the pair on the same lawn they first forged their partnership on -- which Booth romantically recalls in his vows -- to a Cyndi Lauper serenade, the ceremony was a beautiful tribute to the pair’s history, capped off by Brennan’s vows, the letter she wrote to Booth while buried alive seven years prior.

“Dear Agent Booth, you are a confusing man,” she reads. “You are irrational and impulsive, superstitious and exasperating. You believe in ghosts and angels and maybe even Santa Claus, and because of you, I’ve started to see the universe differently. How is it possible that simply looking into your fine face gives me so much joy? Why does it make me so happy that every time I try to sneak a peek at you, you are already looking at me?”

Photo: FOX

“Like you, it makes no sense. And like you, it feels right. If I ever get out of here, I will find a time and a place to tell you that you make my life messy and confusing and unfocused and irrational and wonderful,” Brennan recounts to her husband, before telling him, “This is that time. This is that place.”

6. “The Hole in the Heart” (Season 6, Episode 22)

The penultimate episode of season six is impossible to mention without alluding to the season finale -- which deserves a similar ranking, if only for Booth’s reaction to Brennan telling him she’s pregnant.

But first comes the tragic telling of how they got to that moment. After the death of intern Vincent Nigel-Murray at the hands of season six sniper big bad Jacob Broadsky, the partners spend the night together at Booth’s apartment, sharing a tearful, intimate moment in the middle of the night that turns into much more.

Photo: FOX

And then the entire fandom turned into Angela:

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5. “The Santa in the Slush” (Season 3, Episode 9)

Bones set the tone for great Christmas episodes with season one’s "The Man in the Fallout Shelter," but this season three romp to uncover the mystery behind a mall Santa’s demise was one of its best, beginning with another appearance from Caroline, who’s feeling “puckish” and blackmails Brennan into getting an uncharacteristically grinchy Booth under some mistletoe, leading to their first kiss! (For now.)

Photo: FOX

Ultimately, Booth’s holiday spirit is saved by a visit from his son, Parker, and the two surprise Brennan and her family by hauling a Christmas tree outside the prison fence so that her father and brother can have a real holiday behind bars. And the rest is heart eyes history.

4. “The Parts in the Sum of the Whole” (Season 5, Episode 16)

OK, so about that first kiss…

Bones’ 100th episode flashed back in time, mostly in service of refuting Sweets’ soon-to-be-published book about Booth and Brennan’s partnership. Turns out, they had worked together once before the pilot’s Cleo Eller case, and what’s more, they kissed back then!

Sweets is horrified by the implications of this reveal, but turns his concern back to the pair’s present day romantic stalemate, putting the pressure on Booth: “It’s gotta be you. You’re the gambler.”

They run out on the psychologist, but outside the office, Booth goes for it, despite Brennan’s protests. “You know when you talk to older couples, who have been in love for 30 or 40 or 50 years, it’s always the guy who says, ‘I knew.’ I knew, right from the beginning,” he insists. “Bones, I’m that guy. I know.”

Photo: FOX

It’s not enough to change Brennan’s mind, though, and you can see Booth’s heart break just one more time when she pleads with him to remain partners. He agrees, but asserts that he has to “move on,” and even though they walk off together, they’ve never been further apart. Truly heartcrushing.

3. “The Doctor in the Photo” (Season 6, Episode 9)

This uniquely suspenseful season six episode saw Brennan overidentifying with a victim, a doctor whose behavior became increasingly reckless as a result of her heartbreaking line of work and interpersonal guardedness. The usually stone-faced anthropologist slowly crumbles to pieces as she puts together the details of the other woman’s life -- which includes a missed romantic opportunity -- culminating in Brennan’s tearful confession to Booth and the heartbreaking realization that she’s missed her chance.

Photo: FOX

It’s one of Deschanel’s most impressive performances of the entire series, and -- thanks in no small part to skillful editing and a guest turn from the always fantastic Enrico Colantoni -- one of those hours that reminds you how unfair it is that major television awards rarely give procedurals much of a second glance.

2. “The End in the Beginning” (Season 4, Episode 26)

One of Bones’ best concept episodes, the fourth season finale gave fans a fresh twist on its usual murder mystery and a taste of Booth and Brennan as a happy couple, even though the real thing was still a few seasons off. The story comes from the mind of a comatose Booth; as Brennan reads to him in the hospital, he imagines a life as a nightclub owner with her as his wife.

Photo: FOX

As usual, the whole squad is there, and as usual, they step up to the couple’s defense when a body is found in their club. From Sweets as a bartender who’s “practically a psychologist” to hostess Angela, bouncer Wendell and chef Fisher -- plus, Zach! -- “Mr. B” and “Bren” soon realize that their employees would do anything to keep them from being implicated in the murder, even if they didn’t do it. All this because everyone knows without a doubt that they’d kill to protect each other.

While the fallout from this hallucination, and Booth’s confusion over what parts of it were real -- as an extra blow, dream-Brennan was also pregnant with the couple’s first child -- would reverberate throughout the pair’s relationship in season five, looking back at it now as just another one of their wild stories is sweetly nostalgic.

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1. “Aliens in a Spaceship” (Season 2, Episode 9)

The Grave Digger’s first episode is also one of the series’ best, and a true classic for the show’s central couple. As Brennan and Hodgins contemplate romance and mortality while buried alive in a car underground -- later writing goodbye letters to the people they care for most -- Booth and Angela desperately lead the team in putting the pieces together to find their loved ones.

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Finally successful, the team arrives just in time to see Brennan and Hodgins attempt to blast their way to the surface, and watching Booth sprint across the quarry to drag Brennan from the rubble is the stuff that true TV love is made of. That Brennan’s farewell note to Booth returns, seven seasons later, in her wedding vows, proves just how meant to be these two always were.

Honorable Mention: “Pilot” (Season 1, Episode 1)

Boreanaz has oft-cited this as his favorite episode, and it’s easy to see why. Though the characters have certainly evolved through the seasons (the first episode aired on Sept. 13, 2005!), the pilot episode sets up the squints we grew to know and love, and the show’s dynamic duo, right from the start.

Photo: FOX

Booth and Brennan’s chemistry is palpable from their first scene together -- what woman wouldn’t love a man who calls Homeland Security to have her detained? -- and despite a bit of retconning later in the series, their first case together is the beginning of a beautiful partnership.

Honorable Mention: “The Conspiracy in the Corpse” (Season 10, Episode 1) and “The Scare in the Score” (Season 12, Episode 7)

It’s nearly impossible to put the episodes that feature Sweets and Max’s heartbreaking deaths on any kind of “best” list, but credit where credit is due for the couple’s “baby duck” and Brennan’s father -- two men who became some of their closest family throughout the years.

Photo: FOX

“Sweets is a part of us. Our lives, who we are at this very moment, have been shaped by our relationships with Sweets,” Brennan says of the psychologist at his memorial service, which is attended by just his Jeffersonian family -- including Daisy, who’s expecting their first child. “Each of us is like a delicate equation, and Sweets was the variable without which we wouldn’t be who we are.”

Much of the same can be said of Max, who, like Sweets and Pops, knew what was happening between Booth and Brennan even before they did. When Brennan’s fugitive father came barreling back into her life in season two, it was Booth who first protected her and then helped her reconcile, forging a tense respect with the future father-in-law he would also try and arrest more than once.

That Max dies while protecting his grandkids from a killer seeking vengeance on Booth -- after Brennan pleads with him to stay with Christine and baby Hank at the FBI safe house -- is perfectly tragic and tragically perfect.

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