Johanna's murder board

In "Flowers for Your Grave" (1x01), Castle tries to run a profile on Beckett, and inadvertently hits on the fact that she's lost someone close to her, the case was never closed, and this is why she became a cop. It's taken a long time, but slowly the mystery of Johanna Beckett is beginning to unfold.

In "A Chill Goes Through Her Veins" (1x05) Castle picks up on the man's watch Beckett wears and asks if it was her father's, assuming he was the person she lost. At the end of the ep, she tells him the story and we find out:

* Kate and her father were supposed to meet her mother for dinner at a restaurant, but she never showed up. Two hours later, they went home and a Detective Raglan was waiting for them to tell them she'd been murdered.
* Her purse was there with everything in it, and she hadn't been assaulted.
* She'd been stabbed several times and it was attributed to gang violence. No one was ever caught.
* Kate's father fell into alcoholism, but has been sober 5 years as of S1. She wears her dad's watch, presumably to mark how long that's been ("for the life I saved"), and a ring that belonged to her mother on a gold chain beneath her clothes ("for the life I lost"). The ring is visible from ep 1x05 till about ep 2x21, and then for reasons that are never explained, Beckett stops wearing it. She does wear the watch in every ep, including the pilot.

Further developments in subsequent episodes:

* A number of people have suggested the ring is Johanna's engagement ring, but the stone is blue, rather than diamond, and the setting looks like it might be a family heirloom. When she's not wearing them, Kate used to keep the ring and the watch in a memory box with her parents' picture embedded into the lid, along with her badge and her gun; this may have been lost when her apartment blew up in "Boom!" (2x18). In "A Death in the Family" (1x10), Castle gives the file he got from Esposito (1x05) to his friend, Dr Clark Murray, a pathologist, hoping he can shed some light on something that was missed.
* Johanna was stabbed four times. In 1x10, Murray comes back and explains that this was not random, that the first stab went to her kidney and the knife was twisted. This would have put Johanna into immediate shock, and is the wound which killed her. The others were 'for show'. Murray believes Johanna was targeted for a reason, and has found three other murders which took place around the same time, all of which were dismissed as random. The connection between the four murders appears to be more complex than a serial killer -- according to Murray, they were all targeted.
* The other three victims were one of Johanna's former students, a documents clerk, and a lawyer for a non-profit organisation (Murray tells this to Castle in 1x10, but the audience doesn't get the information until 2x01).
* Kate tried to investigate the murder herself for the first three years she was on the force, with no success. The resulting stress drove her close to breakdown and she spent a year in therapy before finally accepting that she needed to 'let it go'. She does seem to have made a kind of tenuous peace with the fact that she will probably never know what happened -- in "Home is Where the Heart Stops" (1x07), a young woman whose mother has been murdered asks how she deals with it, and Kate answers that it doesn't really get any better, but she has gotten as far as not minding carrying it around. In "Sucker Punch" (2x13), the knife wounds on a victim catch Lanie's attention, and she calls in Dr Murray for a consult. They turn out to match the pattern and the weapon that murdered Johanna Beckett.
* Beckett herself doesn't seem to have shared the details of what Castle found in 1x10 with Lanie. Castle started to tell Lanie in 2x01, then they were interrupted. This means that at some point he and Lanie must have continued that conversation, or she took it upon herself to check the file.
* Both the knife and the tactic used to kill Johanna are used by Special Forces.
* Beckett catches the actual person who carried out the hit, a drug smuggler named Jack Coonan, but has to shoot him to protect Castle before she can get him to tell her who ordered her mother killed or why.
* Coonan does intimate that the order came from way on high, and that it's a can of worms Beckett should not open.
In "Knockdown" (3x13) Beckett reveals the murder board she's been building for her mother's case, inside the shutters of one of the windows in her new apartment. Facts from the murder board answer a lot of logistical questions we've had no information on before.
* Johanna Beckett was murdered on Saturday, January 9th, 1999. Terri Miller tweeted that at the time Kate was 19 years old and her birthday is November 17th, so she was born in 1979 (she turned 19 on November 17th, 1998), was a freshman in college, and is indeed 29 at the start of Season 1.
* In 1x05, Beckett says her mother never showed up for dinner and when she and her father got home, the police were already waiting for them, so the implication is that Johanna's body was found almost immediately. But (oopsie) the crime scene photos were taken in daylight, even though it would have been dark by dinnertime in January.
* In 3x13, Raglan, the detective on Johanna's case, was involved in covering up Johanna's murder and admitted this to Beckett just before he was killed in front of her by a sniper, Lockwood, working on orders from above. The whole thing stems back to something very bad he did 19 years ago, 7 years before Johanna was killed, which involved the shooting of an FBI officer in the same alley.
* Johanna was a civil rights attorney, who also worked with a group called the Justice Initiative, which did pro-bono work for 'lost causes'. All of those murdered at the same time were part of the group. They had apparently been investigating the murder of the officer, believing the man put away for it, a mafioso named Pulgatti, was innocent (at least of that crime).
* Johanna's body was found in an alley on the Lower West Side.
* She had also been heading up a "Take Back the Neighborhood" campaign in Washington Heights (which is way way uptown, around 155th Street), trying to get drug dealers off the streets. The implication in the ep is that she was killed in the same neighborhood where she was campaigning, so the Post-It may be an oopsie because the two neighborhoods are miles apart.
* The others were murdered at different times, in different parts of town: Jennifer Stewart on Friday, May 21st, 1999 in Central Park; Diane Cavanaugh, Sunday, March 7th 1999, near 65th and Amsterdam; and Scott Murray, Sunday March 7th, 1999, behind a bar (no other location visible on the card).
* Johanna had requested a court file just before she was murdered, but no trace of it was ever found.
* Beckett says her mother had a code she used for keeping appointments, but it was so complex she and her father were never able to break it, so they're not entirely sure where Johanna was in the weeks before she was killed.
* Johanna took pictures of the alley where her body was found about a week before she was killed, but they're not in the packet of photos with the others on the roll.
* In "Knockdown" (3x13), Lockwood, a new hit man appears, killing Raglan (who has a fatal disease and wanted to come clean to Beckett before meeting his maker) in front of Castle and Beckett, and abducting and torturing Esposito and Ryan in an attempt to find out how much Beckett and Montgomery know. Castle and Beckett rescue them and, after Castle leaps on Lockwood to stop him shooting Beckett, the shooter is arrested and jailed.
* Beckett has apparently been visiting Lockwood once a week to see if he's cracked. Needless to say, he hasn't.
* The second cop, McCallister, is murdered by Lockwood in prison, on orders from the Big Bad. Lockwood escapes while in court to be arraigned.
* Roy Montgomery is revealed as the the cop who shot the FBI agent, Bob Armen, a rookie error he's been atoning for ever since. He's also been protecting Beckett by making sure she never got too close to answer; a deal he seems to have made directly with the Big Bad.
* In "Knockout" (3x24), Lockwood escapes with paramilitary-style help, and Beckett throws all caution to the wind to try to catch him, with disastrous results.
* Montgomery is shot by Lockwood, in a confrontation which he ends by killing Lockwood with a hidden gun.
* Before going to meet Lockwood, Montgomery packed up about half a dozen police files and sent them...to someone, thinking this would continue to protect Beckett once he's dead.
* While delivering the eulogy at Montgomery's funeral, Beckett is shot in the chest by another sniper, suggesting the Big Bad isn't done cleaning house yet.
* In "Rise" (4x01), Castle, Ryan, and Esposito try to figure out who shot Beckett while she recovers over the summer. She wants to jump right back into the case on her return.
* Beckett's shooter managed to escape the cemetery, presumably by dressing as a groundskeeper and walking away unidentified in the chaos. He left behind his weapon - a Mark 11 modified sniper rifle. It's clean for prints, but the serial number shows it was the never-recovered gun of a Navy Seal that was killed in action 7 years ago.
* It's been three months without a lead on Beckett's shooter. Because of this, the 12th's new Captain Victoria "Iron" Gates has shut down the investigation, which Beckett refuses to accept.
* Castle suggested they look into the bank where Raglan, McCallister, and Montgomery were depositing their ransom money. They find the bank, but it's out of business and all the account files had been moved to a warehouse in Union City.
* Three weeks after Johanna Beckett's murder, the warehouse that held the files from the defunct bank caught fire. An investigation ruled the fire was accidental due to faulty wiring.
* Before his death, Montgomery was using the files as collateral to keep both his family and Beckett safe. If they got out, they could harm some very powerful people.
* Those files were mailed by Montgomery and were received by someone with the last name of 'Smith' after the funeral and Beckett's shooting. He's apparently got connections; after he receives the files he places a call (from a burner phone) to the United States Congressional Offices. He also calls Castle and tells him that Beckett can be kept safe provided she stops looking into the case.In the middle of investigating a murder connected to the Mayor in "Dial M for Mayor" (4x12), Castle gets another call from Smith, the man who Montgomery mailed files to before his death and who tells Castle they again need to talk.
* Smith apparently has ears inside the Mayor's office because he gives Castle clues that lead them toward the actual killer. He also knows (before Castle and Beckett) that the Mayor was right in thinking there is a conspiracy against him.
* Mayor Robert Weldon was looking to advance his political career, looking towards running for governor in 2 years and then maybe President of the United States in 6 years, but it seems being associated with this murder conspiracy has effectively stalled his career.
* After the case is over, Castle contacts Smith again to find out why he called. Smith tells him (in not so many words) that he had to ensure Castle stay in the precinct to make sure Beckett 'doesn't look into things she shouldn't'.
* Smith is vague about why he's determined that Beckett stay safe, only saying that in chess sometimes "a well placed pawn is more powerful than a king".
* In "Always" (4x23), Montgomery's house is broken into and personal files pertaining to his old cases are stolen, along with his old laptop and his wedding album, prompting Beckett to tie the murder of the thief to her shooting and her mom's murder.
* The victim has DNA under his fingers, which turns out to be from a man using the alias Cole Maddox. The same DNA was also found at Beckett's shooting and is a match to the man who shot her.
* Smith calls Castle again, warning him that they still hold the cards as long as Castle can keep Beckett from looking into her mom's case or her shooting.
* The files that were stolen from the Montgomerys' house lead Maddox to Smith. In the end Maddox threatens Smith, telling him that he knows that the files Montgomery sent him before he died were blackmail and he wants that information. And after he gets it, he's going to "put Kate Beckett in the ground where she belongs".
* Beckett seems to have made peace with letting her shooting and her mom's case go after fighting with Maddox on a rooftop and almost dying again, telling Castle that "he got away and [she] didn't care". Big breaks in the case come in "After the Storm" (5x01), after they find the photo Maddox was after in Montgomery's wedding album. This leads them to find the identity of Smith and the contents of the files Montgomery mailed to him. Most importantly they discover that the man who was in on a cut of the bribe ring Montgomery, Raglan, and McAllister were running is (then ADA) William Bracken, now a senator up for re-election. Smith was a lawyer that owed Montgomery a favor and that's the only reason he held the files that kept Beckett safe.
* Maddox gets to Smith to try and find and destroy the files, but in the process beats Smith badly. Smith survives surgery but is killed in the hospital after someone phones the officer standing guard and tells him to leave.
* Smith had two copies of Montgomery's file, one in his apartment and one in a floor safe at his office. Maddox gets to both files first, but Smith rigged the second file to explode if it was moved. This explosion kills Maddox.
* Beckett and the gang piece together enough of the scattered pieces of paper to find the account number (0862241) where the money was being deposited. The account was closed in 1993, but it still has the name William H. Bracken attached to it.
* Bracken was Assistant District Attorney from 1988 to 1992, which coincides with the years Montgomery and company were holding mobsters for ransom. He realized there was nothing he could do about it, so instead he asked for a cut of the ransom money in the form of money orders made out to cash. He used that money to fund his first congressional run.
* The theory is that Bracken is cleaning house now and killing all those people that know about the scandal because he's being groomed to run for President of the United States.
* Beckett confronts Bracken at a fundraiser and strikes a deal with him for her safety and the safety of those she loves. Hopefully it sticks.
* In "Recoil", the death of an intern involved in Bracken's election campaign leads to a possible threat on Bracken's life, and he requires Beckett to personally guard him until the suspect is found. She's forced to decide whether to save Bracken or betray her badge by letting him step into harm's way.
* Beckett is tasked with going undercover to bust a drug dealer only known as Lazarus in "In the Belly of the Beast" (6x17). When things go south she tries to keep her cover by going deeper into their organization.
* Vulcan Simmons is heading a drug operation that is laundering tons of money through into an account called "Future Forward". He's originally believed to be Lazarus. Simmons orders Beckett killed because she was "playing in a world [she] doesn't belong, just like [her] momma".
* She's saved from death by a hired assassin sent by the real Lazarus. When questioned, Elena only says she was sent because Lazarus owed Beckett and wanted her to live.
* The team realizes that "Future Forward" is a super PAC account that is being used to fund a political campaign.
* Later at home, Beckett sees a press conference with Senator Bracken where he announces his intention to start a campaign to be President of the United States. She connects the dots: Bracken is Lazarus and he's using drug money to fund his political campaign. He's also the one that saved her from the assassin, because he owed her for saving his life in "Recoil" (5x13), but now they're even and she's no longer safe.
* Johanna Beckett's case comes to head in "Veritas" (6x22). Castle and Beckett have been trying to expose Bracken as dirty by watching Vulcan Simmons. Beckett goes on surveillance alone when one of her people of interest comes back into town. Beckett backs off when she realizes that it's a bad idea to be going at it alone. She's at a standstill until their person of interest, Jason Marks, ends up dead.
* Marks' death leads Beckett to try to pin the murder on Vulcan Simmons, hoping to get him to confess to laundering money for Senator Bracken. Beckett confronts Simmons alone in a garage where she's found the evidence that will incriminate him, but he doesn't back down, and we don't witness the end of their conversation.
* Vulcan Simmons turns up dead the next morning. He was shot in the knees and shoulders before being shot in the chest. Ballistics reveal that the gun that killed Simmons was a .40 caliber registered as Beckett's backup gun that she keeps in her safe in her apartment.
* On Esposito's hunch, Castle and Beckett hunt down the doctor that signed Michael Smith's death certificate. He claims Smith died in the hospital, but when they're leaving Castle gets a call from Smith on a burner phone. Smith explains he faked his death to stay alive and in the meantime has been looking for a recording of Bracken confessing to murder. It turns out he also made contact with Jason Marks, who was about to roll on Bracken's dirty finances when he was killed. Now he has to start over because he has no informant and no tape. Smith suggests Beckett run, otherwise Bracken will kill her.
* Castle and Beckett take Smith's advice, but before they can get out of town Bracken shows up at their motel room. Beckett is alone and he laments that she couldn't let the case go, but now he has to tie up loose ends. His thugs try to dose her and get her drunk to make her murder look like a suicide, but just as they're about to pull the trigger she fights back, killing both thugs and escaping.
* Beckett remembers her first meeting with Montgomery, who had hinted that Beckett should be looking for evidence in her mother's personal possessions. The memory has her convincing Castle to turn around and they head back to her apartment, but they don't know exactly what they're looking for and her mom's notes are all coded and aren't much help. Internal Affairs catches them and arrests them along with Ryan and Esposito, who were standing lookout.
* Just as they're about to be taken to booking, Beckett realizes that her mom's note might have hinted to the location of the tape being in the elephant statue she keeps on her desk. It's a last ditch effort that pays off; a mini-cassette tape was hidden there all along.
* The tape reveals Montgomery leading Bracken into confessions that he blackmailed Raglan, McAllister, and Montgomery, and also that he had people killed before. He also mentions that he wouldn't hesitate to have Johanna Beckett killed if she kept poking around. It's the evidence Beckett needs to arrest Bracken.
* Senator William Bracken is arrested by Kate Beckett at a press conference in Washington, D.C. It looks like it's over. Beckett has won.