Credit: Patrick McElhenney/Fox

Bones is at its best when the show takes a more serious tone.

Tonight’s episode started off in its now-typical light-hearted fashion. Booth (David Boreanaz) makes Brennan (Emily Deschanel) watch a basketball game, and she obsesses over Phil Jackson’s coaching techniques and his ideas on teamwork. She gathers all the interns together to help them form a more cohesive bond, instead of fighting for her admiration. While they are working to identify remains in the Jeffersonian, they come across a homeless man whose death was overlooked by the police. They come to find out that he was Tim Murphy, a Gulf War veteran, who died from injuries sustained while saving people in the 9/11 attack on the Pentagon.

Here are my favorite parts of the episode:

Hodgins (T.J. Tyne) abandons his conspiracy theories.

“I have looked into every 9/11 conspiracy. All of them. None of them hold up. Or I should say only one of them does. We were attacked by extremists who hated everything we represent. We might not be angels, but no one deserved to die that day. No one.”

Booth’s dogged determination to find the identity of the victim.

“We went to Afghanistan because of those attacks. No matter how bad it got, we would never leave anyone behind.”

Arastoo (Pej Vahdat) rebukes Finn (Luke Kleintank) for assuming Arastoo is upset because he is Muslim, too.

“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,” Arastoo says.

“Thank you. I’m sorry. And thank you for taking the time to set me straight,” Finn replies.

“Yeah, that was awesome, dude,” Fisher (Joel David Moore) adds, for a bit of levity.

The interns share where they were on 9/11.

Fisher: “I was in high school. It was my senior year. I was breaking into my history teacher’s desk to steal a test that I hadn’t studied for. And he walked in and he was crying. He couldn’t care less what I was doing. That’s when I found out. So I talked to him. A stolen test in my hand. We both just sat and we cried.”

Clark (Eugene Byrd): “I was working. It was before school. A coffee shop. Everyone was just staring at the TV. No one said a word. The cook came out to watch with the rest of us. I still remember the smell of food burning on that grill.”

Finn: “I was nine. I had gotten in the way of my step-father hitting my mama and he stuck me with some scissors. My mama wanted to take me to the hospital. But my hurt didn’t seem like nothing, after we heard what happened.”

Arastoo: “I was at morning prayers. I didn’t believe that day. I didn’t believe in anything that day.

Wendell (Michael Grant Terry): “I was with my aunt, from that morning for the next few days. My uncle was a firefighter in New York. He never came home.”

The funeral.

Booth, a former Army Ranger, gives an impassioned speech. “For years, Tim Murphy was homeless. He was forgotten He was one of those people on the streets that we try not to look at because the sight of them is just too painful. But we’re all cut from the same cloth. Tim knew that. He knew how connected all of us are. He knew that if it wasn’t for his three buddies, that Tim wouldn’t be alive on September 11th, to save the lives of Diane, Warren and James. And we wouldn’t be able to tell Tim’s son that his dad didn’t die a broken man living on the streets … but he was as brave and noble as the best of us. We lay him to rest today a hero.”

Bones and Booth’s exchange at the end.

“I dug out remains from the rubble of the towers. For two weeks, I was methodical. A scientist. I did what was asked of me. I did my job. I never shed a tear. I was proud of that. All of these years, I never let myself feel it,” she says.

“Bones, we all deal with things in our own way, OK?” Booth explains.

“I could avoid it all before I met you. I had no one in my life. And now I think of those people and I think of you. Any one of them, could have been you,” Bones says.

What did you think of how Bones handled 9/11?