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The Blacklist is just an excuse for Reddington to get close to certain criminals as part of a larger scheme.He got some sort of coded message from Wujing, and discreetly stole a photo from the Stewmaker's collection of past victims. Red is working on some sort of master plan, everyone seems to agree on that, but for him to pull it off he needs to get to the people on the Blacklist, and he's using the FBI to eliminate them in order to cover his tracks.
Reddington's daughter is dead, and he's trying to replace her.Keen's past sounds like Reddington is her father, but it's a coincidence. His real daughter would have ended up like Keen, a successful law enforcement officer despite her terrible family background. Except that she was killed on the job and Reddington was somehow responsible. He's trying to deal with the crushing guilt by adopting another daughter figure.
Season One will end with Liz having to kill Tom. Season Two will have her in the process of grieving and moving on with her life.
Berlin is Liz's grandfatherThe story about Berlin that one of the prisoners told is true. Berlin's daughter fled to America where she gave birth to Liz. Reddington was hired to protect them but he failed and the Stewmaker took Liz's mother, and tortured and killed her on behalf of Berlin's enemies. Liz was supposed to have died in the fire but Reddington rescued her and placed her with Sam. However, Berlin believes that Reddington sold out his daughter and is seeking revenge. It is all a tragic misunderstanding.
Keen's husband is the Big Bad or at least the first season end gameReddington is going to use Keen to take down her husband and then direct her to take down her father.
Reddington is trying to prevent an massive event that will kill millions.Early in his criminal career he became unknowingly connected to a massive conspiracy to kill millions of people. Finding out about it he started working to prevent it by becoming one of the biggest criminals in the world and establishing connections to thousands of criminals and other people and started out planning a massive gambit to destroy the conspiracy. With him turning to the FBI being him starting to execute the plans. With Zamani actually knowing about the plans and having been convinced to sacrifice his life to stop the conspiracy from happening. Basically being the ultimate example of Even Evil Has Standards.
Tom Keen isn't a criminalHe's a CIA agent who was told to protect Elizabeth, though not necessarily told why. Which is why somebody trained like him would get beat down like he was in the first episode - he has no idea how in over his head he really is.
Reddington will claim to be Keen's father.He isn't, but it will be an excellent way to manipulate her.
Keen's husband is on The Blacklist.That's how Reddington knows about him and that's why he picked Keen as his partner.
Reddington really is just doing this for the hell of it.He keeps using the word "fun" to describe his work with the FBI. ("Let's call it The Blacklist, that sounds fun." "Ah, what fun.") This is probably meant to sound like a smokescreen for his true motives, but in reality, it's the truth. There's no grand scheme behind everything; Reddington just decided one day that being a master criminal was boring. After all, where's the fun in planning brilliant crimes if there's no one smart enough to even pose a challenge? He thought that watching the FBI dance as they tried to catch the people whose names he gave them sounded like a good time. The reason he'll only work with Keen is because he saw something in her that made him think she'd be a fun partner.
Reddington wants to train KeenHe found someone with a psychological profile that he liked, and now wishes to train her to become more like him. However, he wants her to take his methods and fix them. He takes pride in what he does, but also sees the problem areas and is molding her to fix his formula.
Keen is Reddington's daughter.Same as above, but not illegitimate. Reddington is shown to be quite clever, so he could have erased himself from their records. Or Keen's mother, to distance herself from Reddington's new reputation kept that information from her child.
Reddington is a Glory Seeker.He's just decided that going down as the guy who destroyed organized crime the world over would be a great way to get into the history books. Once he's finished the list, he'll simply disappear, assuming he doesn't manage a pardon.
Red killed Sam to keep Fitch's secrets safe.The "truth" that Sam said Lizzy deserved to hear includes one of the secrets that Fitch wants to keep safe. That's why Red told Sam "I can't let you do that" and why he had to kill him. This also ties in well with the above theory that Tom is working for Fitch, and why Tom traveled ahead of Lizzy to see his father in law (her father): to check if Sam lets anything slip on his deathbed. In fact, perhaps Tom already knew that Red was going to kill Sam, and doesn't realize Red is on to him. (Though that last one seems unlikely, obviously Tom knows his cover was nearly blown.) Either that, or Tom was sent to kill Sam if he blabbed, and Red ended up doing it for him.
Keen's Mother is the true villainWe've had no mention of her. Ever. We know more about Reddington's wife than Keen's mother. Perhaps she ordered Reddington's family killed and is the leader of the organization Tom works for. Keen is valuable for her biologic connection to the woman but also because of childhood memories that are locked in her mind. Keen became a profiler chasing these memories at least at some level. Her biologic father died protecting Keen from her mother after he found out who she really was. Her father was possibly a criminal in her mothers organization. Red and Tom are waiting for the information that Keen can reveal when she uncovers her memories. Red will use them to take down her mother and seek revenge. Tom is in place waiting for this possibility as a sleeper cell and will kill Keen and Reddington over the information. Keen isn't dead because her mother wants her alive unless she uncovers her real childhood.
Keen's father is Reddington's rivalHe's taken an interest to mess with the guy.
Keen isn't Reddington's daughter — she's his daughter in lawHer husband is Reddington's illegitimate son. Alternatively, since we know Reddington had a daughter, Tom was Reddington's daughter, but transitioned into a man. That's why he and Elizabeth are looking into adoption, instead of trying for biological children. Elizabeth doesn't know about her husband's past. Reddington thinks it's wrong for his son to keep such a big secret from his wife which is why he keeps telling her not to trust Tom.
Reddington has been working for the US government all along.His entire criminal career has been part of a CIA undercover operation to gather together as many international criminals and terrorists as possible so that the FBI can get them all in one swoop. It simply isn't time for him to reveal his cover yet, though at least one of the agents assigned to him is probably his handler.
Fitch is Liz's father.Red is trying to protect Liz from Fitch and his Nebulous Evil Organization, which is why he started working with the FBI in the first place. And Tom is one of Fitch's agents, which is why Red warned Liz not to trust him.
Red was brought into Fitch's organization, and discovered seriously horrible things that caused him to go rogue.This is why:
Keen's father was Reddington's mentor/bossThe guy who hand picked him and taught him everything he knows about being a criminal.
Keen's father was Reddington's protegeBut he got killed or defected and he thought his most promising students daughter would be a good candidate to replace him.
The "Farmer" that Reddington refers to in "The Stewmaker" is himself.Red talks about a "farmer" who comes home and finds everything that made life worth living in ruins. In his despair, a "life's work" comes from his "knotted mind" and one day looks back and sees the damage he has done, and that he has to pay. When Liz implies that the farmer couldn't help himself, Red disagrees that such a man could ever make amends. Which sounds like the Stewmaker except for the fact that Red has never met the Stewmaker before, and didn't know his name until earlier that day.Who else do we know who might fit that description?
Keen is Reddington's illegitimate daughter.Already this theory is circulating the interwebs as a likely explanation for why he insists on only talking to one young female agent - and an extremely green one at that.
Reddington initially disappeared because he discovered something he shouldn't have.He was an intelligence officer in the US Navy who abandoned his very promising career and family out of the blue. While on the job, he probably discovered something that would have made the US goverment look very bad if it was found out, so to protect himself and his family he goes on the run. Eventually, the need for both money to support himself, as well as allies to protect him from the military, causes him to sell secret documents that he is able to access to some unsavory people, thus beginning his Start of Darkness. Essentially, Reddington is Bradley/Chelsea Manning before the internet and with fewer morals.
Reddington is Keyser Söze from The Usual Suspects.James Spader's role oozes Kevin Spacey.
Reddington is a Watcher from Fringe.Possibly the first or the base for them. He is bald, has a similar taste in clothing, and is a master at setting up insane plans on seemingly coincidence. Also is basically unstoppable as it all goes according to plan due to things he has no way of possibly knowing.
Reddington is her uncleOr was otherwise very close to her father (brother or best friend), got him killed and now feels responsible for the child he left behind.
Agent Dickweed, er, Ressler, is actually Mike from Homeland, and is also somehow behind everything on both showsHe changed his name and then inserted himself into the FBI so that he could watch everything up close, and he's gonna somehow get Brody on the blacklist and then point the FBI to his little hideout in Caracas, after which he...does something devastating, or tries to until Spader, er, Red, hams him to death. Also, they really, really look alike, almost as if they're played by the same actor (Diego Klatenhoff).
The series is set in the same universe as The Dark Knight SagaAnslo Garrick and The Chechen ("MEY DAWGS! ARE! HUNGRAY!" guy from the Dark Knight) are played by the same person, and so are Lau (The Chinese accountant) and the Wujing. Therefore The Dark Knight is actually simply the story of the Wujing and Anslo Garrick working together in The Con. So:
Sam and Red were both in Fitch's organization.This is how Red knows Sam, and why he (presumably) picked Sam, who probably did not go rogue, to raise his family for him. Sam knows the same secrets as Red, and has been living with them all this time. This would also suggest that Tom was inserted into Lizzie's life in order to serve as a failsafe/threat for Fitch to use should Red go too far, since they can't kill Red because he has his secrets triggered by his death. The Emergency Stash is for use if and when Tom has to "pull the trigger," so he can make a fast escape. The gun being linked to the Boston assassination is deliberate to throw the authorities off. This also means Tom knew about the cameras all along. They were installed after Red made contact with Lizzie so that they could monitor her, and perhaps also to ensure Tom goes through with his mission if needed. Another theory; while Sam, Red, and Tom all worked with Fitch, Tom is a later recruit, so Fitch figures Red isn't onto Tom, but Red knows due to his deep connections. Possibly through Sam, who presumably did not go rogue when Red did. Actually, this would explain why Red surrendered himself to the FBI, because he found out about Tom and realized that Fitch had made a move on his family. Literally Red came out of hiding to protect Lizzie from Tom and the blacklist is just collateral to kill time "above water" without being in jail. The more I think of it.... This is why on his first day out of hiding, he has already made a deal with Zamani to send a torturer after Tom — to give Fitch a warning right up front that his sleeper agent is vulnerable and that he is onto him and he can also pull out some creative hits/ops too. This would also probably mean that Gina Zanetakos is/was also in Fitch Org, which is how Red knows she was Tom's lover, and why even though she spills the beans about everything she has done, she denies knowing Tom, because she knows he is a sleeper and even though she is out of the game she cannot expose other agents, perhaps for her own sake or for the sake of her own loved ones a la Lizzie for Red.
Reddington's Story in "The Judge" is true...He didn't abandon his family, they were slaughtered and left for him to find. There was a massive coverup of the blood bath. Red went rouge to seek revenge and uncover the truth ever sense. This explains the story with Ressler in "Mako Tanida" and Red's empathy with loosing loved ones. Red and Dembe are bonded over their families blood spilled at their feet, as this is the implied story due to Dembe's slave past. This also explains Red's ballet flashback with who we can only suspect is his daughter, especially in conjunction with the dancers gossip. Also explains destroying his family home. All of his body guards and Keen (even if she doesn't remember fully) have this in common and he will never fully trust someone who hasn't had this experience.