After Abby's ex-boyfriend, Chad DiMera left town, she began to focus more on her family. Abby became concerned for her cousin, Nick Fallon, who left town, but didn't check-in with any of his family members after he got settled. In reality, Gabi Hernandez, Kate Roberts and Sami Brady murdered Nick after he tried to rape Gabi and they covered up the crime. Abby started to look into the events surrounding Nick "leaving town" and she came close to figuring out something happened between Nick and Gabi before he left.
EJ, who was protecting Sami, went to the Horton cabin to convince Abby to let the issue go. E.J. and Abby ended up fighting, which lead to the two of them sleeping together for the first time. Their affair didn't stop there, as the two found it hard to stay away from one another. Everyone was shocked when an alive Nick showed up at Arianna Horton's christening. Sami encouraged E.J. to stop Abby from talking to Hope Brady about Nick's disappearance, which threw the two of them together even more.
EJ and Abby had more close encounters. One day, he followed Abby into the hospital supply closet where they almost had sex again, but were interrupted. By this time, Abby couldn't stop thinking about E.J. So, she followed him to his gym. The two had sex in the shower and Sami walked in. E.J. came out to talk to Sami while Abby stayed hidden. Abby heard Sami talk about the fact that E.J. and Sami weren't sleeping together at the moment, and she started to realize that she was only sleeping with E.J. because Sami wasn't.
E.J. tried to explain to Abby that she had nothing to feel bad about. He accepted most of the blame for their affair. But, he reiterated that what happened between them was a mistake. He was in love with Sami. Eventually, Abby conceded that their affair was over. Abby experienced a pregnancy scare, and thought she had become pregnant from her affair with EJ. However, she was relieved when the pregnancy test came back negative, and what she was experiencing was just a flu bug.
Sami eventually found out about the affair and planned a huge revenge scheme. She exacted revenge on EJ and Abby both. Her revenge plans went on for months, until she finally forgave EJ and they reconciled. Abby also moved on and began a relationship with Ben Rogers.