Things took another major turning point in E.J.'s life after baby Grace died of bacterial meningitis in June. Sami was still unaware about the baby switch and told E.J. the "truth," in that Grace was actually his baby who died. E.J. felt betrayed, angry, confused, and bewildered by this revelation and mourned a child he never got to know. He vowed revenge on a grieving Sami and presented her with custody papers, forcing her to hand Johnny over.

A guilty Nicole continued to keep mum about the baby switch and managed to convince E.J. to drop the custody suit against Sami.

E.J. took Nicole on a honeymoon in Paris. Unfortunately, Arianna Hernandez overheard Brady and Nicole talking about her miscarriage. She confronted Brady about it, and he called Nicole to to warn her. Brady was unaware that E.J. answered Nicole's phone. He blurted out that her secret was out. E.J. soon confronted Nicole about what secret she was keeping. Nicole tried to cover up her lies by claiming that Brady was on drugs again, but soon revealed one half of the truth: she miscarried their baby nearly a year ago, and Sydney wasn't theirs. However, she kept mum about Sydney being E.J. and Sami's baby. E.J. demanded to know who Sydney's real parents were. He soon realized that Dr. Baker helped Nicole cover up her secret and get her a baby. After Stefano had a heart attack which was related to his diabetes, E.J. kicked Nicole and Sydney out of the mansion.

E.J. got into a heated confrontation with Brady over helping Nicole cover up her lies.

He received a visit from Chad Peterson Woods, who announced that he was Sydney's father. Little did they know that Sydney was switched with Grace at birth, and Grace was really Mia and Chad's daughter.

E.J. was unaware that Stefano had known the truth about the baby switch for a long time and had been conspiring with Nicole to keep Sydney's parentage a secret. Former FBI agent Rafe Hernandez was getting closer to finding out the truth about Sydney, so Stefano decided to put a hit out on him. Fortunately, E.J. saved Rafe's life. Rafe soon figured out the baby switch and secretly tested DNA on Sami and Sydney. When he got proof that Sydney was indeed Sami's baby, he revealed the truth to Sami and brought Sydney back to her. Sami angrily confronted Nicole over switching babies, and Nicole was forced to reveal to E.J. that Sydney was indeed his and Sami's child. Nicole was arrested, but Brady bailed her out, and Brady was unaware that Nicole knew all along that Sydney was E.J. and Sami's child.

E.J. soon realized that Stefano knew about the baby switch all along. He confronted his father and nearly strangled him. He declared that he was moving out of the mansion, cutting all ties with Stefano, and intended to never let Stefano see his grandchildren ever again. Meanwhile, Brady urged Nicole to make amends with the people she hurt. Nicole went to the mansion to find Sydney alone in her playpen while Sami and E.J. were in the other room arguing about Sydney's living arrangements. She snuck in and took Sydney, and E.J. and Sami were horrified to discover that their daughter was gone. They concluded that Nicole took her.

Nicole and Sydney ended up in Cleveland. She called E.J. and warned him that he would never see Sydney again. Afterwards, she called Brady, who urged her to do the right thing and bring Sydney back. Nicole soon called Sami, but during the phone call Nicole was knocked unconscious at the bus station and someone kidnapped Sydney. Rafe discovered Nicole was in Cleveland. E.J., Sami, Brady, and Rafe soon headed to Cleveland in an effort to find Nicole and Sydney. E.J. angrily confronted Nicole in her hospital room and made threats, but she swore up and down she didn't know what happened to Sydney. She soon remembered hearing a woman's voice at the bus station and seeing designer boots. Unfortunately, this lead turned out to be a dead end. E.J. and Sami held a candlelight vigil for Sydney on Christmas Eve. It was soon revealed that Anna DiMera was the one who had Sydney. E.J. received a note from the kidnapper and urged Sami not to tell Rafe about the note.

2010

Anna contacted E.J. and Sami and demanded five million dollars for the return of Sydney. E.J. urged Sami to keep the latest ransom note and demand a secret from Rafe. After Nicole went to prison for her baby-switching crimes, it was revealed that E.J. was the mastermind behind Sydney's kidnapping! He and Anna were working together, and E.J. wanted to get back at Sami for keeping his child a secret from him for so many months. He also made it his mission in life to drive Rafe and Sami apart in order to ensure that Sami ended up with nothing. E.J. even made it look as though Sydney was dead after shredding her bloody dress and tossing it into the river, devastating Sami. He eventually had a change of heart and decided to make himself look like a hero by bringing Sydney back to the pub and reuniting her with Sami and the rest of the family.

E.J. grew closer to Sami, who was completely unaware that he kept Sydney from her for months. He was angry upon finding out that the governor pardoned Nicole and freed her from prison. He soon came to the realization that he was still in love with the mother of his children. Will he ever reconcile with Sami? What will she do upon finding out the horrible truth? Stay tuned!