Well, for anyone who’s interested in the resolution but didn’t watch on-line, here’s how it turned out. There were a few improbabilities, but hey, it’s dramatic fiction. 
Leo was rescued from Mexico in last week’s episode. Many dead bodies, including the two original kidnappers.
FBI Agent Archer was behind it all. His son died while waiting for a heart transplant. He found out that Leo Cain got the heart that was supposed to go to his son. Ellie was responsible for that – she either bribed someone or used her family’s friendship with the surgeon, it wasn’t explained.
Archer set out to bring the Cain family down, and used his FBI status to find out about Cain’s business, and he dated Cain’s mistress to get info about his personal life. This took years, and when he had it all together, he decided it wasn’t sufficient to destroy the Cain family. Hence the kidnapping.
He financed the kidnapping using money stolen from a drug raid. I suppose being an FBI agent gave him connections to the bad guys he used, as well as the technology. I should have picked up that it was an inside job 8 episodes ago, because nothing they did went right.
The 9 episodes we didn’t see probably delved more into all the machinations – setting up King for stealing the drug money, hiring Virgil as Leo’s bodyguard, bringing a brand new agent from Alaska to work on the case, killing Claire and preserving her body, etc.
In the last episode, Archer started killing people to cover his tracks. Then he went to the Cain apartment and held a gun on Leo while he told Ellie and Conrad why he did it. In the meantime, King and Knapp had figured out Archer was the bad guy (thanks to dead Claire’s mother). King set himself up with a rifle in the apartment across from Cain’s and shot Archer through a window.
One of the things that really impressed me about the writing was that they showed the after effects on Leo. He didn’t just go home and take up his old life. He was shaking, hugging his mom, having nightmares, etc. The kid’s gonna have a hard time.
I think everything about the show was excellent. The last shot was Kellogg, out of prison, calling Knapp on the phone and teasing him about taking up his old life, so there’s a nemesis for a second season.
Nothing left hanging, except for The Accountant. He’s still out there.