A subplot in "The Wannabe in the Weeds" had a stalker of the victim of the week transfer her affections toward Booth. At the end of the episode, she shows up at the karaoke bar all the characters are at and prepares to shoot Brennan, whom she sees as an obstacle. Before she can, Booth stands up and reaches for his gun and the stalker accidentally shoots him. Brennan goes to him and when the stalker prepares to shoot her, too, Brennan, in one swift motion, picks up Booth's gun, shoots the stalker in the neck, and goes back to Booth.
Also, In order to keep her father from being convicted of murder and probably receiving the death penalty, Brennan implicates herself in the murder in order to give the jury plausible deniability. It works.
Angela has her own in that episode, when she refuses to testify against Brennan's father:
Angela: I've got nothing to say.
Caroline: You're under oath as a material witness, Ms. Montenegro.
Angela: I swore to tell the truth, and the truth is that I am not saying anything.
Caroline: Judge Haddoes, could you ...
Judge Haddoes: The witness will answer.
Angela No, the witness will not.
Brennan: Angela, answer!
Judge Haddoes: Silence, please. The witness will answer, or will find her in contempt.
Angela: (to the judge) Is there any way that I could talk you out of that?
Judge Haddoes: Why would you call a witness you knew wouldn't answer?
Caroline: I figured once she got up here and saw your scary face she'd rethink her options.
Angela: I'm taking the Fifth.
Caroline: Chérie, the Fifth refers to the Fifth Amendment, which protect you from being forced to incriminate yourself.
Angela: Okay, alright, well, the First Amendment protects freedom of association, right? Which means that it protects friendship. So I'm taking the First. Which, is even better than taking the Fifth.
Judge Haddoes: There is no friendship in a homicide trial! This is he Federal District Court for the District of Columbia, United States of America! When this asks you a question, you answer, or you pay the ferryman.
Angela: It ain't gonna happen.
Bones and Booth have been questioning a gang leader, who, true to form, has been hitting on Bones the entire interview. While they're waiting by the elevator, Bones provokes the guy into grabbing her arm in an aggressive manner, which is technically assault. She then proceeds to beat the snot out of him in "self-defense". Booth: "Feel better?" Bones(breathing heavily): "I think I do, yeah." At the end of that episode, said gang leader has put a hit on Bones. Booth tracks him down, shoves a revolver into his mouth, and orders him to take the hit off, or he'll kill him.
"The Pain in the Heart": Brennan convincing Zack to give up Gormogon by pure logic. Logic which proves he's not a sociopath.
The second episode has one where Brennan confronts the killer, who is dousing a room with evidence in gasoline. When Brennan says she can't let him destroy evidence, he pulls out a lighter and does the whole "try and stop me and we both burn" thing. Brennan immediately whips out her revolver and shoots him in the leg.
There's one episode whose subplot has the team undergoing security evaluations. The last one is Bones. Pickering asks her about a certain incident in her past. Bones picks up the phone and dials a number.
Bones: Hello? This is Brennan. you told me to call this number if anyone asks about...him.
Then she hands the phone to Pickering. By the time whoever's on the other end gets done, Pickering is looking rather disturbed.
Bones: Are we done?
Pickering: Yes. In fact. The entire review is suspended. I'm to stay here until someone comes to burn my notes.
Greg Dored, the victim from episode "The Bond in the Boot", was an unassuming CIA analyst who managed to break his ankle twice trying and failing to complete an entry level obstacle course. However, when he picked up chatter about a plot to smuggle contraband into the country and his boss refused to act on his information, he went rogue on his own. By himself, he took down a Ex-Russian special forces soldier who was acting as a courier, hid the contraband and sent his girlfriend an encoded picture with the location so that it could be found after his death. He was then captured by the group who wanted whatever they had smuggled into the country. They bound his hands and feet together and hung him up in a position known as "the swallow". He then had over 24 holes drilled into his arm with a diamond cutting laser. Throughout it all he never talked and was eventually kept in the torture position so long that he asphyxiated and died. The CIA was so impressed by his loyalty and sacrifice they retroactively made him an agent so that they could honour him with a star on their wall of unnamed fallen Agents.
In the episode "The Hero in the Hold", Brennan and Sweets are interrogating the Gravedigger. After she finds out where she hid Booth, Brennan starts to walk out, picks up a briefcase, turns around, and smacks the living HELL out of her, drops it, and walks off.
In the episode "The Princess and the Pear", Sweets and Brennan are run off the road by a Black Knight. Sweets gets knocked out, and the Knight steals the Excalibur sword from their backseat. Brennan manages to get out of the car and proceeds to kick the Knight's ass and disarms him of the sword.
Booth gets one in "The Proof in the Pudding" when a pack led by the Smug Snake "Mr. White", commandeer the lab and refuse to let the team do their work properly. Booth decides that We Need a Distraction. He starts off by cuffing Mr. White to a rail and flipping him over it...
Booth: You know what, your job is to protect the president, mine's to solve murders. * heave*
He then leads Mr. White's thug squad on a merry chase through the lab, dispatching them with nothing but handcuffs and his own considerable skills. One Genre Blind agent thinks he has the upper hand...
Agent: (* arrogantly* ) What d'ya got, Feeb?
Booth: * Groin Attack* Good old American classic in my hometown. * cuff*
Andrew: Ten seconds earlier I would've been the hero, right?
Bones and Hodgins finding ways to prolong their air supply and signal their location while buried alive in "Aliens in a Spaceship."
Booth also gets one later on in the episode when he digs Brennan and Hodgins out of the ground with his bare hands!
At the beginning of "The Mastodon in the Room", Brennan and Daisy are accosted by a group of armed guerrillas. Brennan's response? Beating the snot out of them with a shovel.
In The Bullet in the Brain, Booth confronts his mentor, Broadsky, who has gone rogue and who is quite possibly the only sniper on earth as good as he is, on private property that his mentor bought under Booth's name, and stares him down cold. He stays on one side of the property line, telling Booth that if he wants the evidence that will prove it, he'll have to cross that line with a search warrant.
Booth: *jumps the fence* I don't need a warrant. This land belongs to Seeley Booth.
Complete with an epic Oh Crap moment from Broadsky and equally epic cocky smile from Booth.
In The Hole in the Heart, Booth and Broadsky's hide and go seek sniper showdown. Booth has pursued Broadsky to his base of operations, a dockyard maze of shipping containers where Broadsky is not only intimately familiar with the territory but armed with a customized precision rifle that insanely outperforms Booth's FBI-approved mass-production longarm. Booth, however, gets one game-breaking advantage - Bones and the Squints, who've been puzzling over some odd cracks in the skull of one of Broadsky's victims for the entire episode, realize that due to Booth's trick shot on Broadsky in their previous encounter...
Booth's eyes light up - With his hand in a cast, Broadsky can only rest the gun barrel on his arm and is incapable of gripping the barrel and aiming downwards.
Booth: You may have just saved my life.
Booth thus goes against his training and stays on the ground, while Broadsky follows that training, takes the high ground, and is left wide open when Booth shoots his other hand before he can change cover, resulting in the CMOA-
Booth: [from out of nowhere] Drop your weapon or I'll blow your head off.
The Human vs. T-Rex arm wrestling match in "The Hole in the Heart," made even more awesome by the fact that the human wins.
A brief moment, but at one point, Bones and Booth consult the chiropractor of the victim. After helping them, Bones thanks him, even though he's not a medical doctor. He immediately fires back that she isn't either. Of course, the chiropractor ended up as the killer, but it's nice to see Bones taken down a peg now and then
Booth gets a big one in the episode "Two Bodies in the Lab" when he risks his life to rescue Brennan from a murderer, despite having just barely survived a freaking explosion!!
Zack Addy had his own Crowning Moment in "The Wannabe in the Weeds", when he told Hodgins that he had taken singing lessons as a child. When Hodgins expressed doubt that Zack could sing, Zack started belting out "Love Is a Many Splendored Thing", drawing an audience from the other Jeffersonian staff members. Before leaving, Angela turned to Zack, mouthed "Wow!" and gave him a thumbs up.
In "The Passenger in the Oven", a woman is murdered on Booth and Brennan's flight to China. The plane is considered American soil until they land in China, so they have to solve the murder while the plane is still in the air or lose jurisdiction to the Chinese. They finally have enough evidence that Caroline can sign the arrest warrant with literally seconds to spare.
Brennan: Booth, I can see people, we have less than 30 seconds!
Booth:(on the phone with Caroline and Cam) Caroline, you gotta trust me on this.
Caroline: Make the case, agent Booth. Something more than motive!
Brennan: Booth, if this missing video game turns out to be the computer chip imbedded in the victim's sternum...
Booth: Where'd you lose the cartridge, Eli? (to Caroline) We got forensic corroboration. The moment this plane touches down, I lose jurisdiction!
Caroline: This better be a good—
Cam: Sign the warrant! Please?
Caroline: Okay! Make the arrest.
Booth: Eli Bilbrey, I am placing you under arrest for the murder of Elizabeth Jones. Anything you say can and will be used against you in a court of law, because this is the United States of America!
(plane touches down)
Arastoo gets one in "The Patriot in Purgatory" when Finn mistakenly assumes that the case at hand (a possible 9/11 victim) was too much for Arastoo since both he and the terrorists share the same religion. Then this happens:
Arastoo: Is it too difficult for you to work with Dr. Edison?
Finn: Um … excuse me?
Arastoo: You share the same religion with men who cherry-picked the Bible to justify slavery.
Finn: I'm sorry. I didn't mean nothing.
Arastoo: But still your words have meaning, don't they, Mr. Abernathy? Those assumptions you made, those quick generalizations. What about the vengeance and the bloodshed in the Old Testament?
Clark: Okay. He's just a kid, Arastoo.
Arastoo: If he's not old enough to know, he's certainly old enough to learn. The Crusades, the Inquisition, are these events guided by a religion of peace? No, they were guided by self-important men who think they know more than the God they claim to worship. This was not the work of religion. It was arrogance. It was hypocrisy. It was hate. Those horrible men who hijacked those planes hijacked my religion that day, too. They insulted my God. So, no, this isn't too difficult. It's a privilege to be able to serve this victim, to show him the care and love that was so absent that day.
Made even better by Finn apologizing and thanking Arastoo for setting him straight.
Booth finally shooting Pelant in the season 8 premiere. Ever since his introduction, Pelant's been walking away smelling like roses whenever he shows up. But this time, as he makes his getaway, Booth manages to line up a shot, and NAILS Pelant right in the head, complete with epic blood spatter and his getaway car careening out of sight. We later see Pelant's Plot Armor kick back in via Author's Saving Throw - Booth's shot misses everything vital, and Pelant just kills a vet during The Stinger to access medical supplies for stitching his face up - but seeing someone finally do permanentdamage to the Smug SnakeVillain Sue was absolutely cathartic.
Much later on, Pelant tries to get Booth to make a Sadistic Choice while he's holding Brennan hostage. Brennan just tells Booth to shoot, and he nails Pelant square in the neck. He doesn't get back up. Booth finally wiped out that son of a bitch.
A Meta one for the writers of The Witch in the Wardrobe. We see a standard scene with Product Placement, in this case a Prius, showing off the "stay in your lane feature". . . which immediately gets Hodgins and Angela arrested and stuck in jail, thanks to some old bench warrants and a sheriff who takes his job very seriously. This leads to Hodgins and Angela reconnecting, leading to their wedding at the end of the episode (while still in jail). Yes ladies and gentlemen, these writers made mandatory Product Placement into an event that permanently altered the dynamics of the series.
"The Pathos in the Pathogens" shows just how awesome the team can be when motivated by one of their own being in danger, when an accident sees Arastoo get infected with the same unknown virus that killed the victim of the week. Hodgins comes up with a way to slow the virus down just enough, Booth drags the killer into the lockdowned Jeffersonian in order to shove his face very close to the victim's bones in order to try to get him to tell them where the cure is (which would be a confession), and, ultimately, Brennan stabs the killer with a needle that she says is full of the virus (which works, because as far as the killer knows, saying nothing would be a death sentence). Brennan was lying about the virus, but she flat-out tells Booth that if she had had a live virus syringe, she would have used it. Do not mess with anyone on this team.
Booth isn't someone to be messed with, especially if he's interrogating. When investigating the death of a former forgein Child Soldier he came across a wanted war criminal. While he didn't get him to confess, it's later shown he didn't need to. As long as the suspect said even a word, Booth would have what he needs to identify him. There is a reason he is the best at his job, people!
Booth in "The Bones that Foam" getting a suspect to reveal the information he needed by driving like a maniac towards a railroad.