Reese wants to get away – he’s at the airport waiting for his flight when he gets a text flight update. His flight is overbooked and they need to change it. One by one we see all the international flights cancelled on the departures monitor that can’t be a mere coincidence. He approaches the ticket window where magically one seat on another flight opens up and it’s first class. Reese can’t help but be suspicious, so he trashes his cell before boarding the flight.
On the plane we meet the first class flight attendant Holly played by Sally Pressman. Reese and the flight attendant encounter a first class jerk who won’t turn off his cell phone, so Reese does what we have all wanted to do at one time or another, he discretely punches his lights out. The phone drops and Reese slips it into his magazine pocket. Holly returns happy to see that the passenger is asleep.
Once the plane is at cruising altitude, Reese gets a text on the jerk’s cell phone. It reads 4C, a message that is clearly for our man in the suit. Reese gets out of his seat to scope out the situation where he clocks two US Marshall’s protecting the passenger of 4C. He slips a knife from the flight attendants cabin, then hears a suspicious noise from the first class lavatory. He finds one Marshall knocked out, his sidearm missing. He calls Harold to find out what this is all about, but Harold doesn’t know what he’s talking about, he didn’t put Reese on the flight, the Machine did and now the plane is over the atlantic heading toward Rome. Reese refuses to take the mission. He intends to inform the other Marshall about the situation and stay out of it. When he does the Marshall tells him to bug off and Reese is more than happy to do so. The Marshall though takes Reese’s warning seriously, but faints while trying to get up. A second later a Colombian stabs the passenger in 4C with a needle, before he can inject the poison, Reese takes him out. Holly comes when she sees two men passed out. Reese says some people just can’t stay awake on planes and asks her to get a few blankets. The passenger in 4C introduces himself as Owen Matthews. Reese says the needle had a coagulant to make his death look natural.
Reese contacts Harold for help, sends him a pic of Owen and tells him the attacker was Colombian paramilitary Lancer and is probably on a drug cartel’s payroll. Harold informs Reese that the Marshalls cracked a case and took down an online drug market called blackmarket bizarre run by a drug lord named The Sphinx. The site only accepts bitcoin and is untraceable. Owen works for the company that hosted the site, so of course Reese wants to know why Owen is in trouble. Owen says he doesn’t know, he’s a nobody, he’s irrelevant. That’s when Reese realizes he’s probably not an irrelevant number but a relevant one.
Harold realizes it too and calls Shaw in for help, he needs her to contact her old bosses with the ISA, so they can figure out why the machine put John on the flight. John isn’t glad to hear that Harold figured out that Owen is a relevant number and kept it from him. He compares Harold to the Machine, someone with all the answers, but never revealing all of it. Reese has another chat with Owen and wants to know why he is a matter of national security. With a little mid-air torture, Owen admits that he programmed the black market site and has met the Sphinx. With the revelation, the dots connect for Reese and Harold as to why the Colombian drug cartel wants Owen dead. Reese decides to leave Owen for a while to use him as bait.
Reese speaks to Holly again to calm her. He tells her he works for the International Homeland Security and everyone on the plane is a suspect so she can’t alert the captain just yet. If she can just do her best to keep everyone in their seats. Reese’s plan works as two more assassins try to kill Owen, he takes care of one easy enough, but the other is able to stab John in the shoulder, luckily for him Holly is there to back him up as she knocks the second assassin out with a fire extinguisher.
In the city, Shaw enters a travel agency that is clearly a front. This is where all of her itineraries came from when she got mission’s to take out a relevant number. Shaw subdues the one agent there and interrogates him to find out why Owen is relevant. He doesn’t know, he just tasks the agents on their missions. The agents number is indigo-six-alpha.
Reese and Holly toss the two assassins into a lavatory. Reese makes sure they won’t wake up by forcing down a couple of sleeping pills down their throats. Harold and Shaw speak with Reese and tell him that there’s an ISA agent on the plane. Shaw was indigo-five-alpha, so this agent is her replacement and as deadly as her, the description of the assassin is tall, dark and wearing a suit, just like Reese. He sees the other assassin approaching Owen and excuses himself. The element of surprise gives Reese the upper hand and takes out the agent with ease. When he turns back to Owen, he’s gone.
Holly is doing pretty well under the circumstances, but still throws back a shot of whiskey. She rants about her job and her coworker, Carlos who doesn’t know what he’s doing. Reese tells her she’s good at her job. Holly thanks him, but wonders what happened to Owen when we hear a sneeze from the lavatory. Owen is just hiding. Reese asks Holly to let them into the cargo hold until the flight is over.
Harold checks in with Shaw to see if she’s figured out why the ISA wants him dead. She hasn’t, but she’s about to sit with Hirsch, so give her a minute. Meanwhile, Reese realizes the reason so many people want Owen dead is because he is The Sphinx. He created the website to revolutionize drug business and decrease drug violence. He makes Reese an offer, but he doesn’t care. Reese hates these computer guys that create programs they think makes the world better, but when it has repercussions they don’t take any responsibility. He’s clearly talking about Harold and he hears Reese loud and clear. They’re interrupted by the ISA agent.
Shaw sits with Hirsch, her drug taking affect on him. A truth serum. He reveals that the ISA knew about him as the Sphinx a year ago, but now that he’s about to testify he became a matter of national security.
Reese continues to protect Owen and confronts the ISA agent in hand to hand combat. Reese uses every possible weapon from the luggage in the cargo hold, but the agent has a better weapon. Reese gets lucky again when Owen knocks out the assassin with a golf club. Harold informs Reese about Shaw’s intel, but it doesn’t explain why the Machine put him on the plane. Harold reminds him that the Machine determines terrorist attacks. The Lancers once took down an entire plane to kill one man. There must be another Lancer on board, but Harold checked the manifest. That’s when Harold realizes the other Lancer assassin isn’t a passenger, but Carlos the flight attendant.
Up on the passenger deck, Carlos brings the Captain some coffee, then with a well timed gun shot that matches the in-flight movie, kills the Captain. Then with one strike, subdues the co-pilot. He takes the wheel and puts the plane on a crash course.
There’s no way into the cockpit. He’ll need Harold’s help. Owen is safely stashed in the cargo hold. Harold hacked into the plane’s computer, but can’t turn on the autopilot while a pilot has it on manual. Reese uses a drink cart to ram the door, he gains access and pulls Carlos from the pilot seat. The two fight while the plane continues to fly out of control. Harold tries one last time to turn on the auto-pilot, but can’t. He’ll just have to take over the manual control and land the plane. Reese finally knocks out Carlos and asks Harold to land them safely. He does to a chorus of applause. None of the pilots are any wiser. Reese tells him that they saved all the passangers on the plane and that was worth it. Holly wonders what Reese really does and he says “he helps people”
At baggage claim, Reese grabs a large case and takes it to a secluded corner to open it and let Owen out. Reese tells him to go to a hotel and wait for Harold. Owen thanks him, but doesn’t understand why he helps people just to help people.
After a quick drink with Holly, she asks him to call her if he ever returns to NY. They say their good-byes and Reese walks over to Harold. He flew in to get Owen situated with a new identity and life. Harold then explains to Reese why he programmed the Machine the way he did. It only spits out numbers so that there is always a human element to make the final decision because humans have free will and with it comes with great responsibility and great lose. He misses Carter dearly too. We know that Reese has already made up his mind. He wonders when Harold is leaving, he responds soon and Reese is welcome to join. He says he’s not sure if he can because he wants to get a new suit. Harold realizes he plans to return. Reese also needs a ride back home. Harold says it’s not a problem, he knows the pilot, which is of course him and can delay the flight for Reese. And like that, Reese is back on the team after an episode long retirement.