The very first episode of the first season of The Blacklist centers around a crashed prison transport plane carrying now-bloodied prisoners. It takes place just outside Manhattan, and the FBI are interviewing what people survived the crash. The whole situation is a tangle of confusion, because initially no one understands where the plane was going or where it came from. One man who can barely speak English explains that a hooded man was handcuffed to a guard, and he was yelling orders at the pilot, and then cut the guard's hand off. The episode then delves into Raymond “Red” Reddington, who is a criminal, and Elizabeth Keen, a rookie FBI agent.
Red turns himself into the FBI after having served not only as a former agent of the US Government but as a long-time enemy as well. Red had been doing business with criminals for many years beforehand, but now he shows up saying that he wants to give his contacts to the FBI. This is what the series is named for—Red's “Blacklist.” Red has one condition, however, and that is that he can work with Elizabeth Keen, an FBI agent. He claims it has to do with a connection to her father. After this point they team up together in order to put a halt to the criminals which are on Red's blacklist.
There is some friction and mystery concerning Tom Keen, Liz's husband and a covert operative. Later Tom is blamed for a murder, and at first all fingers point to Red for framing him, but as it turns out someone else is responsible for all of it. Before the truth is uncovered Liz refuses to work with Red because she believes he is the one behind Tom being framed. This doesn't last, however, as another high profile criminal appears on the scene and they return to working together.
The season ends on quite an intriguing note. A mysterious woman calling herself Jolene enters the plot making advantages at Tom, and while he doesn't give in, he does admit that he loves Liz even though he's targeting his wife because he's a double agent. Jolene and Tom conspire against Red for a strange man who goes by the name “Berlin.” Liz eventually finds out about Tom, as well as Red's true motives to eliminate his enemies with his blacklist. Red comes through for Liz, however, and helps her to find Tom and Berlin—or so they think. The end alludes to the possible fact that Liz is Red's daughter. Needless to say, the first season was very drama-packed and left a very good setup for the second season.
The second season began to prove that all of the name's on Red's blacklist have more to do with both he and Liz than it would appear on first glance. The second season hinges on number twelve on his list, a man coined “The Decemberist.” This man is the primary reason for the conflict between Red and Berlin, as he is the one who killed Berlin's daughter, which Berlin believes Red to be responsible for.