Just outside Manhattan, bloody prisoners stumble from the wreckage of the crashed prison transport plane. No one knows where it came from or where it was going. The FBI is already interviewing the captured survivors, all of whom explain in broken English that a monster guy in a hood who was handcuffed to a guard cut his hand off after barking orders at the pilot. Across town, a bearded man with no hand stumbles into a hospital and collapses. Meanwhile, Agent Martin escorts Red to a Post Office cell and chains him to a chair. This time there will be no trial; Red will simply disappear. Nevertheless, Red tells Martin, Liz has made it all worthwhile. Liz tries to convince Cooper to release Red to help with the case, but his hands are tied, especially since she still intends to quit the task force. Liz appeals to Martin, but he's convinced she and Red are in cahoots and won't let her near him. Later, Martin is displeased to announce Red has a visitor. Fitch is beside himself with this epic failure of U.S. intelligence: no one can figure out anything about the plane. He can't help but think the whole operation was perpetrated by the man going after Red, and to that end, his people are prepared to give Red a fighting chance to escape.
Tom knocks on the door of a rundown apartment, and a man - Berlin - opens the door, asking for the list. Tom hands over a piece of paper with the names of everyone on the FBI's task force. Meanwhile, an angry Agent Martin has Red transported to an SUV. He's hoping Red's killed in the escape attempt, and will only allow him two shots to the jaw. Red makes quick work of Martin and the SUV's driver, and by the time the cops arrive at the scene of the ensuing accident, he's long gone, warning Liz that everyone on the task force is a target. Ressler and Meera are already at a nightclub trying to arrest more of the escaped prisoners. When Ressler is distracted handcuffing a guy named Dimitri, someone slips behind Meera and slits her throat. Liz reports her death to Red, who allows that the FBI's good work has forced Berlin from the shadows. Liz insists Berlin must have gotten their names from Tom. Her father's name was also in Tom's code book - so how is he involved? Red insists Sam's only involvement was as Liz's father. Right now, their primary task is to identify their target: Berlin.
Ressler interrogates Dimitri to learn the whole plane flight was a Russian operation to abduct their own fugitives from all over the world. When Russian Ambassador Constantin Matveyev denies all knowledge, Cooper sends Red to get the truth. Using the Ambassador's beloved little dog as leverage, Red is able to extract the plane's manifest and turn it over to the FBI, which indicates two of three guards on board were killed in the crash. Three more convicts are still at large. One of them has to be Berlin, so Cooper sends the duo to interview the third guard, who's just come out of surgery for his missing hand. The guard doesn't recognize any of the three missing convicts, but he does know something about Berlin: No one knows Berlin's real name, but everyone knows he was a former Red Army Colonel, then KGB. When his daughter fell in love with a powerful dissident, she was imprisoned, so he arranged her escape. To make an example of him, the KGB sent Berlin to a Siberian work camp where he was nearly beaten to death. One day he received a pocket watch he once gave his daughter, which contained a photo of her. A few months later, he got a finger, then her ear, and so on. His daughter was being returned to him piece by piece. Legend has it he carved a knife from her bones and managed to escape - to become a ghost of sorts, hooked on avenging his daughter's death. According to the guard, Berlin was never on that plane's manifest...
Martin meets Cooper in a park to explain that if Liz is willing, the task force can continue. Cooper needs to get her back together with Red. When Cooper steps into his car, he realizes his driver has been killed, just as someone in the back seat plies a garrote to his neck and Berlin crosses another name off his list. Somehow, Cooper survives, and the man with the garrote is captured; but he doesn't want to talk. A physically persuasive Ressler gets Berlin's name out of him: Milos Pavel Kinsky. In short order, Red presents Kinsky's file to Fitch. The only trouble? Neither of them can figure out what Red did to Kinsky to warrant this all-out attack. Red asks Fitch to find Kinsky; he'll do the rest. Later, Red tells Liz that one night an old, scared friend showed up at her father's door. In danger, the friend was leaving town, and a little girl needed to be cared for, since her father was killed in a fire that night. Sam took Liz in, and always shielded her from the truth about her biological father. The only memory Liz has from the night of the fire? Her father pulled her from the flames. All Red will say is that the knowledge of this man's identity will put Liz in grave danger. Red loved Sam. Taking his life was the most difficult of all the difficult things he's had to do in life. But he did it to protect Liz, so there's no way he's going to reveal her father's true identity.
Fitch calls with a location on Berlin, so Red gets rid of Liz and shoots his way through a chop shop to find Berlin in an office. Once Berlin is tied up, Red starts his interrogation, with the help of a few well-placed bullet wounds. Red's most critical skill? Remembering the names of everyone he's ever met. Strangely, he has no IDEA who Berlin is. Berlin allows that he sought Red's weakness for years... and then finally, he found out about Liz, who is currently sobbing in her car in a parking lot outside the hospital where Cooper hangs near death. That's when Tom climbs in the passenger seat and points his gun at her, saying, "Hey, babe." Across town, Berlin is just admitting it was the Beirut incident where Red did him wrong, when Tom walks in with his gun to Liz's head. Berlin orders Tom to kill Liz, and when he pauses, Red shoots Berlin in the head, then walks towards Tom, asking to take the bullet meant for Liz. When Tom fires on Red, hitting his arm, Liz manages to get Tom's gun, and shoots him in the gut. He comes after her, so she fires twice more. Red wants to finish Tom off, but Liz insists Tom's life is hers to end. Dying, Tom apologizes, then whispers something in Liz's ear we can't hear.
Ressler and Liz are packing up Meera's office when Aram presents the coroner's results on a charred body found at the plane crash scene, who it turns out, was the third guard on the manifest. When Ressler insists the third guard was the guy whose hand was cut off, Aram realizes they've made a big mistake. Because of lexical ambiguity, they assumed the hooded man cut off the guard's hand - but the hooded man cut off his OWN hand - he's Berlin! Liz and Ressler run to the hospital, but the real Berlin is gone. Of course, Red already knows the guy he killed - Kinsky - wasn't the real Berlin. But if Berlin thinks Red thinks he killed Berlin, then Red has an advantage. Either way, Red doesn't seem to care. He believes Liz is at a crossroads; it's time for her to make a difficult choice that will change the course of her life. Red will fly away if she wants, or... Liz could prevail, and rise above. Liz chooses to walk away and return to her empty apartment, where she packs her bags.
After hours at Cooper's beside, Ressler sees him move a finger. When the cops arrive at the chop shop, there's only one body to pick up... no sign of Tom. Liz finds Red to confide the last thing Tom told her before he died: her father is still alive. Red insists Liz's biological father died in the fire. Nevertheless, Liz and Red are bound and determined to find Berlin... who is walking through New York City, looking at a photo of a young girl inside his pocket watch. That night, Red looks at the same photo - a photo we've seen him with before - as he takes off his shirt to display his back, which is covered in ugly burn scars.
In the stunning Season 1 finale, Liz is forced to reunite with Red in order to track down Berlin. Alan Alda and Peter Stormare guest star.