It was clear that Elliot and ADA Sonya Paxton butted heads over the cases. They have had many heated arguments that had Sonya slapped Elliot. It was soon revealed that Sonya had a drinking problem and was forced to go into rehab. Sonya did return- sober- to try to resurrect her career and again, Elliot and Sonya butted heads. This time it was over Kathleen's involvement on their case- whether or not to put her on the stand to testify. Sonya did return one more time but had only one scene with Elliot on Skype. Sonya was soon murdered. Elliot arrived at the scene when Olivia was leaving. They hugged before Elliot went on in to see Sonya's body- he was devastated by her death.
I personally thought that their chemistry was so intense that there were sparks and I would even go as far as wanting them do the deed on the interrogation table. I would have cheered them on despite my loyalty to Elliot's marriage.