Bishop and Qasim were finally starting to find a way to balance work and their relationship so that they could see each other more often even with their busy schedules. He started walking her to her desk some mornings so that they could just talk to each other and appreciate those extra few minutes together. They discovered that they are very similar but also very different. For example, they are both adorably nerdy and need "positive thinking space" to work. However, Bishop's idea of a good thinking space is the library while Qasim's is the forest.
Qasim is working on translating a series of phone calls in Pashto, looking for any hidden meanings in them and he feels really blocked in his office.
The team has started to get used to seeing him around more often, luckily Gibbs is usually off somewhere else not at his desk when Bishop shows up for work so that awkwardness can be avoided. This particular morning he was off in some unknown place per usual, but unusually instead of appearing behind them shortly after Qasim left, Gibbs came out of MTAC and told McGee to read the rest of the team in on "Willoughby." McGee is pleased to no longer have to keep the rest of the team in the dark and everyone else is glad to find out who McGee was acting so weird and distracted all morning so far.
Willoughby is a high-risk operation to catch a suspected terrorist who there is no substantial evidence on. Reeves is deep undercover as the copilot of Chen's plane, in attempts to gather evidence and bring the target, a man named Chen, down. Then the operation is compromised, and Chen has a bomb on the plane remotely detonated as an attempt to kill him. Reeves is nearly killed but luckily saw Chen's right-hand man acting suspicious and jumped out of the aircraft before the explosion. The team attempts to let Chen believe Reeves is dead while he is really only at the hospital with minor injuries, but the news that he is alive leaks. Reeves wants to continue working until they bring Chen down, but Gibbs benches him to keep him safe. The operation is to continue but is moving slowly due to the task force of multiple agencies that are working on it. Gibbs wants to get things done immediately, not wait for the rest of the task force, and Vance gives him the right away to do so but tread lightly because they still need the task force.
Meanwhile, Bishop visits Qasim's office to deliver mail that was mistakenly given to her instead of him due to it being from the NSA.
"I was given to me by mistake," Bishop says as she walks into Qasim's office holding up a package.
"Those would be my newest calls to translate."
"Mhm. So I need to ask you-"
"If I was able to find any hidden meanings in the calls?" Qasim interrupts, "None. All they are doing is talking about trips they've been on: Paris, Amsterdam, Cairo, etc. I really need to get out of this office, maybe take a trip to the forest."
"Actually... I wanted to see if we could reschedule our date from tonight. I'm in the middle of a case and will have to work late if not all night. Speaking of I should get back to work," she starts to leave.
He gets up and begins following her, "Ellie," she stops and turns back towards him, "are you okay?"
"Yeah," she says assuredly but then says, "Yeah, it's nothing," with a little less confidence, then finally brings down her wall and says, "I saw that Reeves put himself as his emergency contact. Why would someone do that?"
"If it helps, I wrote you," Bishop looks at him quizzically, "for my emergency contact I put down your name."
"Really?"
Qasim shrugs, "Maybe Reeves only wrote himself because he has nobody else to write."
Bishop just nods solemnly.
The team concludes that Chen's pilot must have somehow discovered Reeves' plan and tipped Chen off because they have proof of a transmission from the pilot to Chen right before the plane blew up. They believe that Chen is planning and new attack and is working hard to find out more about it so they can stop it, but he and his right-hand man have gone entirely off the grid making tracking their plans extremely difficult.
On the way to talk to the pilot's family in an attempt to get more information on his work with Chen, Bishop begins to explain her concerns about Reeves.
"You have been talking to me about the same thing for the past 10 minutes, yet you still haven't begun to make any sense," Gibbs says, stopping outside of the conference room to give Bishop one last chance to tell him what she is trying to say. He genuinely cares about whatever she finds so important but also doesn't have time to figure her rambling out in the middle of a significant international case.
"What I'm saying is I don't think Reeves has very many friends and out of the ones he does have I am one of the closer ones and yet he never told me he planned on volunteering for a life-threatening operation."
" You're worried about him."
"Yeah."
"Why didn't you just say that in the first place?"
"I thought I did." She says more to herself than to him as she follows him into the conference room."
During their discussion with his wife, they discover that the pilot had flown Chen to the same locations that the people in Qasim's communications were discussing, tying the two cases together. Qasim had mentioned that the people talking in the phone calls he was translating, discussing these locations when he was talking to Bishop the previous day, and she connected the dots. She informed Gibbs of this possible connection, and they both went to visit Qasim in his office to get more information. Gibbs decides this is a relevant similarity between the two cases and asks for copies of Qasim's translations of the calls. He then has Reeves come over to his house to look over them with him since Reeves had a better perspective due to his direct contact with Chen's organization.
While Reeves study Qasim's translations, Gibbs talks to him or more accurately listens.
"I didn't mess this up. I thought over everything I said, and there is no way that I tipped off the pilot to what I was doing."
"Okay."
"I can take care of myself, I don't need you to worry about me."
"I don't, if you want to risk your life then I say that's your business, but Bishop does worry, and I consider that my business."
"Do you know what Bishop refers to you guys as? A family. That's why I signed up for Willoughby because I don't think you guys should have to do missions like that. People who have people shouldn't have to do things like that. I don't have people who will miss me."
"When you think you're alone in the dark, close your eyes and remember the good."
The correspondances refer to Reeves, making it clear that Chen must have known about Willoughby for weeks even months before the explosion, not mere minutes like they thought. And that the correspondences are happening after the task force meetings, and therefore, there is a mole in the task force, the pilot wasn't the leak.
Bishop goes to the library where the ping she had Abby do on Qasim's phone says he is, to deliver the most recent call that he needs to translate.
"Ellie!" Qasim says, looking up from his laptop and seeing her, "What are you doing here?"
"You weren't at your office, and your phone was going straight to voicemail, so I had Abby ping your phone and found out you were here."
"I got pinged?!"
"Mhm-hmm."
"That's so cool!"
"Now why I came was to give you the recordings from last night." She says while handing him a flash drive.
He takes the flash drive, "Oh right."
"You're doing a great job by the way."
"Really?"
"Yeah, we even caught the mole leaking information to our terrorist thanks to a tip you gave us."
"Thank you, that helps. I've been trying to figure out any hidden codes and have come up with nothing."
"But you tried the library."
"I did, and I love it."
"I just had a bunch of plants delivered to your office so that you can have your own little thinking forest."
Qasim stands up and walks over to her grabbing her hands, "Thank you."
Suddenly, gunfire erupts, she dives for the ground, but he is hit before he can do the same. She goes over to him and then calls 911, going with him to the hospital when the ambulance arrives. She is panicking, and it is apparent she loves him very much and doesn't want to lose him.
They take him back for surgery, and she can't go with him, so she calls and updates Gibbs. He tells the rest of the team, then sends Ducky to be with her, so she isn't alone. Everyone else continues working even more determined now to bring down Chen.
They discover that having been told by the mole that Qasim was translating the communications, Chen sent his second-hand man to kill Qasim so that Qasim couldn't translate the most recent correspondence. Gibbs is putting pressure on the team to be quicker and give him information immediately wasting no time before getting to the point. Abby and McGee work together and prove that the second-hand man did the shooting, so Gibbs has Quinn and Torres go get him, but he kills himself to avoid them getting any information from him.
With no immediate action, they can take against Chen, Gibbs, and Reeves go to the hospital to provide Bishop support and see how Qasim is. When they get to the waiting room, Bishop is in Qasim's room, so Ducky informs them that Qasim has been declared braindead. Gibbs has to sit down to process this information and looks like he is trying to think what he should do next, what would be the best way to support Bishop right now. Ducky tells Reeves that Bishop has been asking for him, so he goes to Qasim's hospital room.
He doesn't say anything just walks over towards her, and she gets up to meet him halfway holding up the flash drive she had gone to the library to bring Qasim.
"The last recording he was supposed to translate," she says as she hands him the flash drive.
He takes it but asks, "Why are you giving this to me?"
"I don't know why but I know you are willing to do anything to get Chen... so am I."
He starts to leave, then turns back and asks, "Would you like me to stay with you?"
"No... I just... um... I don't know how to say goodbye to him."
Maybe you could try closing your eyes and remembering the good."
"Did you learn that from Gibbs?"