Ex-government agent and one of the FBI's Most Wanted fugitives, Raymond "Red" Reddington mysteriously turns himself in to the FBI and offers to give up everyone he has ever worked with including a long-thought-dead terrorist but under one condition - he'll only talk to newly-minted female FBI profiler, Elizabeth Keen with whom he seemingly has no connection. For Liz, it's going to be one hell of a first day on the job and what follows is a twisting series of events as the race to stop a terrorist begins.
Red predicts an impending catastrophe, rooted by the work of an assassin, called "The Freelancer." Together, Liz and Red go undercover to prevent from having his next target, Floriana Campo from being killed. Elsewhere, Ressler and newly re-hired CIA agent, Meera Malik, who's been added to Red's private security detail, keep an eye on them from a distance. Meanwhile, Liz considers what she should do next concerning Tom and the mysterious box she found hidden under the floorboards.
The FBI is on the hunt for a high-ranking Chinese spy, Wujing which Red claims has hired him to help decode a classified CIA transmission. Liz, posing as an FBI cryptographer goes with Red to decode the message while protecting US government secrets. Meanwhile, Liz proactively investigates Tom.
While continuing her investigation into the truth about Tom, Liz testifies against drug lord, Hector Lorca. Later another witness is abducted when he is forced to testify against the dangerous drug trafficker. Red's interest is peaked and he informs the team that the witness may have been taken by "The Stewmaker" a man responsible for hundreds of missing and presumed dead people. Meanwhile, in an unlikely twist of events, Red and Ressler must work together for the first time.
Red finds out that The Courier - a middle man that no one crosses - is delivering a package worth millions of dollars to an Iranian spy. Only the Courier is a ghost no one including Red, knows what he looks like. While racing to stop the mysterious criminal transaction, Liz , inadvertently finds herself thrust into a dangerous kidnapping plot. Meanwhile, Ressler must finally accept that Liz is a valuable asset to the team.
After Tom confronts Liz about the box - he claims he's innocent and insists that they turn it into the FBI so his name can be cleared. Elsewhere, Red informs Liz and the FBI that the next name on the Blacklist is beautiful and deadly corporate terrorist, Gina Zanetakos.
After a chemical attack on a subway, Liz and the FBI search for the man responsible. Liz reluctantly calls on Red for his help after she finds her search for the next person on the blacklist, brilliant scientist Frederick Barnes, heading to a dead end. Meanwhile, Liz wants nothing to do with Red after he implicated Tom.
Liz uncovers an elaborate plot to destroy the country's financial system when a new name on the Blacklist is revealed by Red. Meanwhile Tom supports Liz when a family member falls ill.
Donald attempts to protect Red from a possible assassination attempt but is misled. The newest member on the blacklist, Anslo Garrick, infiltrates the FBI black site and tries to capture Red. Meanwhile Liz gets caught in an elevator and tries to figure out what is going on.
Liz infiltrates the blacksite and disarms the signal jammers to call in backup but runs into trouble along the way. The fate of Ressler hangs in the balance as Red tries to bargain with Anslo Garrick. Meanwhile, Tom becomes increasingly worried about Liz' situation and the fate of Red is unknown.
The entire FBI team is under investigation as internal affairs tries to find the mole. Elsewhere, Red is missing and conducts his own investigation into who betrayed him. Meanwhile, a serial killer from Liz's past, "The Good Samaritan" strikes again. Liz is allowed to join the hunt for the killer as Cooper knows Red will likely reach out to help knowing how much this unsolved case means to Liz.
The team goes undercover to pursue the Alchemist, who uses science to transform DNA and who's been assigned to protect a mob informant. Elsewhere, Liz targets an unlikely couple; Tom and Liz's relationship is tested; and Ressler faces a big decision.
After a recent spate of abductions of babies from their mothers, Red informs Liz that the "Cyprus Agency" is the illegal adoption organization responsible. Coincidentally, Liz and Tom contemplate adoption of their own which fuels Liz to track down the organizations CEO, Owen Mallory.
Liz helps Tom come to terms about their impending adoption while Red reveals that a woman from his past, Madeline Pratt is the next target on the Blacklist. Elsewhere, at an elaborate party at the Syrian Embassy, Red convinces Liz to pull off a covert heist.
When a prominent Prosecutor is found after being missing for 12 years Red believes that this is the work of Ruth Kipling also known as "The Judge." Only a myth, the Judge runs an underground criminal appeals process in which those who have wrongly imprisoned and punished others are judged and punished themselves. Meanwhile, Red investigates the woman who tempts Tom while in Orlando at a teacher's conference.
The next target on the Blacklist is one of Red's past associates, crime lord Mako Tanida. After Tanida escapes from prison he is out for revenge. Elsewhere, Tom confronts Jolene after interfering with his mission.
When a new cyber defense asset gets stolen all roads lead to a Russian cyber terrorist known only as "Ivan". With Red's assistance, Liz discovers a huge cover-up. Meanwhile, new evidence surrounding the disappearance of Jolene helps unravel some of the mystery behind Tom.
Red and the team are on the hunt for "The Undertaker" - a life insurance claim adjuster who convinces ordinary people to become contract killers. Meanwhile, Liz works with Red to uncover Tom's secrets.
The Pavlovich brothers specialize in abductions of high value targets and according to Red, they are planning their next hit. While the team tries to protect the next target, Red has a job of his own for the Pavlovich Brothers. Elsewhere, Liz patiently tries to uncover the truth about Tom.
After a Politician in Prague is framed for a murder, Red suspects it's the work of The Kingmaker - a strategist behind the rise of some of the world's most powerful politicians. While Red helps Liz and the FBI catch him, Liz uncovers a secret that Red's been keeping from her.
Liz refuses to work with Red after discovering the truth about the death of her father. Seeking to make amends and force Liz to see him, Red brings the FBI a case they can't ignore. Meanwhile, Liz reveals what she knows about Tom's secret life to the FBI.
With the crashing of the mysterious prisoner transport plane, the city is on lock down as the authorities are on the hunt for all the escapees. Meanwhile, with Red in custody, Liz uses her power to get him out since he is their best chance at finding all the suspects. Elsewhere, their main objective is to track down Berlin, a prisoner on the plane who is somehow involved.