Spoilers ahead for The Undoing finale. Many viewers suspected that Jonathan killed Elena from the beginning, but The Undoing's finale episode confirmed it. A flashback showed Jonathan going to Elena's studio after the fundraiser and having sex with her — two facts he did admit to throughout the season. Then they had an argument that turned deadly.
Elena mentioned that she and Grace were planning to hang out and that she thought Henry would be a good friend for her son Miguel. Jonathan became angry and told Elena that if she didn't stay away from his family, he would hurt her. She didn't believe him. "You'll never hurt me and you will never leave me," Elena said. Jonathan seemed to want to prove her wrong, and he repeatedly shoved her into the wall. He then walked away and said he was leaving her. At this point, Elena mustered the strength to grab her sculpting hammer and charged after him. But Jonathan pulled the tool away from her and used it on her instead.
After the reveal, fans took to Twitter to joke about how they'd attempted to accuse everyone from Grace to Henry to Grace's friend Sylvia to no avail. The most obvious answer (Jonathan) was right all along.
By the end of the season, Jonathan's wife, son, and lawyer all believed that he was a killer. The most compelling piece of evidence was the discovery of the murder weapon. Jonathan had carelessly disposed of it in the fireplace at Grace's father's country house. Henry found the hammer, and that's when he knew his father was guilty. And when Grace found out that Jonathan hadn't felt any empathy after his younger sister died when they were children, she was done defending him, too. She worked with her friend Sylvia to tip off the prosecution about Jonathan's remorselessness, which almost certainly sealed his fate at his trial.
We didn't get to see how Jonathan's trial ended, but considering that he kidnapped his son and tried to escape to Canada, he probably knew it was over for him. The series concluded with Grace helping to rescue Henry from his father's clutches and the police putting Jonathan back into custody. When his trial resumes, he'll most likely be read a guilty verdict. Spoilers ahead for You Should Have Known by Jean Hanff Korelitz.
For fans of the book the show is based on, the ending was especially unsurprising. In the novel, Jonathan is also the killer. The series gets to that revelation in a different way — he also flees town and never returns, instead confessing in a letter to Grace — but the end result is the same. It was always Jonathan.