I know Lydia kill put hits on other people, but what reason did Walt have to kill her specifically? Walt didn't know there was a hit put on him until after he picked up Todd's phone after Todd was dead. ??
Long story short, Walt killed Lydia to protect Skyler and the kids.
She was presumably the only Madrigal employee still working on the meth operation.
My theory: it goes back to why Walt killed the prisoners and lawyer in S5E8. They may have been in prison, but they knew too much, and they would have ratted at the first chance given to them. And since they didn't have any business to offer, why keep them around? But Lydia was kept alive because of her methylamine, as well as her ties to Europe. But even in that same episode, Lydia was worried about her own life because she was afraid of being in the same spot as the prisoners, "just another someone who knows too much."
And by the series finale, that's exactly what she was. With Jesse free and Todd's gang killed, there was no one left to produce blue crystal with a 92-6% purity. With no production for the business on her end, she became exactly what she feared: just another person who knows too much.
As someone above wrote: "Walt is too complex". Yes, he IS. I often thought I had him figured out and then he would pull some stunt or act in weird way, such as very selfish or macho. Remember his sudden confrontation with Hank at the poolside party after his good diagnosis, when he lets Junior drink? He is enraged by Hank's presumption that HE is the right one, not Walt, to decide how much JR. can drink. Granted, it's messed up, arguing over how drunk to let a teenager get, but he resents Hank for trying to rob him of his role as father and take away his control (a HUGE thing for Walt!).
So I think Walt's killing of Lydia is simple revenge, for what she's put him through. In the finale, notice how he refuses to let Uncle Jack bargain his way out of instant death by telling him where the money is? AND how he stands back and watches with satisfaction as Jesse kills Todd? He is settling accounts, regaining the last bits of control in his life before he dies.
I lost my original post, so hopefully this one will show up. Walt kills Lydia to put an end to his blue meth production. It's not so much fear of who she knows or protecting his family, but to end blue meth production once and for all. Gretchen and Elliot have already removed his contributions to their company, Gray Matter. So what does Walt have left? What will his legacy be? We know the idea of legacy is important to Walt from the episode where he talks to Walt, Jr. about his own father. Even if it's never reported, the police will probably figure out that he killed Jack's gang and ended the production on that end. By getting rid of Lydia as well, blue meth will never show up again, especially in Europe as Walt knows that Jesse will not willingly make meth again. Killing Lydia and Jack with his gang ended blue meth production and that will be Walt's legacy...even overshadowing the $28 million that Gretchen and Elliot gave for meth addiction treatment. A man does what a man does even when no one knows and he is unloved.
Walt had a host of reasons to get rid of Lydia - she was a threat to his family, which he was no longer able to protect (and she's already shown she has no qualms getting rid of people, regardless of the size of the threat); she was both the distributer of the blue meth and a potential supplier of methylamine; she was an extension of Jack's gang, who'd killed Hank and stolen Walt's money... there weren't any reasons not to kill off Lydia, really.
By the end, Walt only had one goal - to ensure his family's protection and solvency, and the only way to do that was to take out everyone who was a possible threat. If he was that worried about his meth legacy, he'd have killed Jesse, the only other person who knew the recipe and could make it as well as him. After all, even if he was convinced that Jesse would never cook again, he would never have been able to guarantee that Jesse wouldn't pass on the recipe to anyone else. I like to think that Walt probably figured Jesse would never cook again, but if he decided to, and wanted to use their old recipe - well, he'd bloody well earned it, hadn't he?
It's not like Walt didn't go to kill Lydia before. He took the ricin to their meet-up in "Gliding O'er All," where she said she was terrified he would kill her as just "another loose end" after she gave him the names of Mike's men. Walt pretends he doesn't know what she's talking about, and they cut a deal ("you need to learn when to accept 'yes' for an answer, Lydia.") She leaves, he picks up his hat, and we see actually paranoid Lydia was correct (just as broken clocks are right twice a day) because he actually HAD brought the ricin with him to do her in after getting the names.
But he spared her at the time because she offered him an in-road to drug sales in the Czech Republic.
So Walt actually had planned to killed her for a long time. He no longer needed her, I think she irritated him (with her whininess), she should have died 2-3x earlier but had been spared for some reason or another, and she had also proven herself a threat to his family if he let her live as she had taken steps in the past to remove those she was paranoid about. "No loose ends." Walt is a stickler for thoroughness, if anything. He finished her off as part of being thorough + some personal dislike. It made him feel good to get closure, as well as "win" their personal match.
Like Walt, Lydia was also the one who would go for the kill to make sure she is not leaving any suspects behind and Walt knew it. Eg. she wanted all of of those 9 men dead as they were a threat to her. After Walt there would be no one to protect his family. And Walt had to ensure that there is no one threatning his family after he is gone. Walt knew that Skyler has seen Lydia as Walt's former asscociate and Lydia can do anything to save her ass. So Walt eliminated Lydia before she could do anything.
I think he did it to stop the operation in case things didn't go as planned when he goes to kill the people who have Jesse. If he fails, they still won't have their Europe connect anymore. Or maybe he just did it cause she was a bitch, but Walt is smarter than that. He did it because he was thinking ahead.
I think Walt changed after his last conversation with Flynn. Walt had spent the series concerned with making money (at all costs) in order to leave his family financially secure. But Flynn, clear sighted and uncorrupted, made him realise the other implications. Walt was effectively leaving his children to face all the drugs, corruption, greed and violence in the world surrounding them. He had, quite literally, brought it all to his own doorstep. He had to put things right before he died. For this reason, evil Lydia had to go along with the rest of the gang. If Jesse had become a partner then he would have had to go too. But because he really had given up producing meth (willingly), and because he was protective of children then he was allowed to live. (This is the same reason the witers and the audience wanted Jesse to live) At the end Jack thinks he still has a chance because Walt doesn't know where the money is, but Walt shoots him because the money is no longer the most important thing.
No habeus corpus. She was told, as her sickness was beginning, what exactly she was poisoned with. Usually those poisoned by such a rare thing as licin don't have the luxury to get the doc right on it so... it saying Deceased on this page isn't true albiet how logical it might seem. Perhaps she'll be around in Saul's forward story.