Elliot and Kathy's marriage was not always perfect. They had their own fair share of problems, mainly with Elliot's job. It wasn't the general role as a cop that Kathy didn't like- it was the amount of hours that Elliot wasn't home and failure of communication. Elliot was very protective of his family, he wouldn't let that world touch his family despite no all-time surveillance but he didn't have to be their window. The point was proven when Maureen witnessed Elliot helping out other cops in discovery of a murdered man and she was shaken. Kathy was also having some jealousy over the amount of time Elliot spent with his partner Olivia and being able to talk to her about the case. Elliot was aware about the amount of time he spent with Olivia and wasn't happy about it himself. It was rare for Elliot to talk to Kathy about work- more so regarding cases of children.
A year before their separation, Elliot told Kathy about a young boy who was found eating out of the garbage cans. He called Elliot and Kathy told him to go check on him. Kathy understood why Elliot was a cop; she knew he was determined and wanted to help, and get justice. Then, all of the sudden, Lorna Scarry (an attorney) outed Elliot's marital status in Don's office when her client accused him of sexual assault. Her private investigator discovered that Kathy filed for legal separation and moved in with her mother, taking the children. The job was making Elliot difficult to live with and Kathy was tired of him being angry all the time. Elliot went to the Priest for counseling but the next thing he knew she wanted out. Elliot has done what he was supposed to do: he got a good job, he never cheated on his wife, and he lost his children! It wasn't supposed to happen but it did.
Elliot was angry at Kathy: he couldn't understand how Kathy could walk away after 20 years of marriage. Elliot wasn't burnt out on his marriage while Kathy bailed, cutting him loose without a clue. Although Kathy has been giving him clues! Just three years previously, Kathy felt that Elliot was shutting her out while Elliot just wouldn't talk about his day at work as the cases seemed like it was getting worst than the last; one of them has to sleep at night. However, Olivia disagreed; if he kept that up, Elliot would lose the best thing he ever had. It turned out she was right. Elliot would often spend the night at the crib, refusing to go home as it was empty (unless Don made him) and calling his children wasn't the same. Although Kathy encouraged Elliot and the children to spend time together, Elliot threw himself into his work and hardly saw his children.
The separation was hard on the children: Kathleen was arrested for a DUI after making an illegal U-turn and Dickie got suspended for busting a kid's lip. Kathy eventually started divorce proceedings- Elliot got the papers but didn't sign them right away. When Kathy was looking for a divorce lawyer, one suggested using the Silver Bullet stratgey where a wife accused the husband for abuse to tip the balance in her favor. But she didn't hire him. After months, Kathy went to see Elliot at work to talk to him, mainly about Kathleen's latest drama. However, Elliot noticed that Kathy had more to say. Kathy wanted to know why he hadn't signed the divorce papers yet? Elliot wouldn't talk to her or her lawyer. The kids were asking if they were going to get back together but she ran out of things to say. She wanted an answer: Elliot didn't know. Kathy accepted it for now until enough time passed when she got more determined.
Kathy then turned to Olivia, meeting at the park. Although they were getting a divorce, Kathy did still cared for Elliot; a piece of paper doesn't change anything but Kathy knew Elliot well enough that he needed to be on solid ground to move on. Olivia gave him stability to help him. Kathy used to worry about Elliot prefering to spend time with Olivia than with her and the kids, but it wasn't true. Elliot used to talk about her all the time. But, Olivia knew things about Elliot Kathy would never understand and that's what she was counting on: she wanted Olivia to talk to Elliot to sign the papers. If she did it without consent, it would be expensive and take more time. But Olivia didn't talk to Elliot. He eventually realized that when love warps into hate there's nothing they wouldn't do. Elliot didn't want Kathy to ever regret him. He left the divorce papers in Kathy's mail box late at night, ringing the doorbell before leaving. Elliot saw Kathy coming out and found the papers. She saw him get into his car and drove away. But the divorce never came through. Elliot wanted to come home.
A year after they had their fifth child, Elliot and Kathy hit a rough patch. Elliot didn't want to talk to Kathy when she tried calling him, wanting to know when he was coming home. He then went undercover and didn't alert Kathy. Instead, Olivia went over to notify Kathy. But she couldn't take it anymore- she had been sleeping on it before. While packing a bag for herself and Eli, Olivia was trying to comfort Kathy, reassuring her that she'll tell Elliot to call her. Kathy caved in and stayed with Elliot. After that close call, Elliot got much better. He may not open up as much but Elliot got more attentive to his family.