In December of 2006, Sami Brady and Lucas Roberts went for a romantic winter vacation when a terrible storm hit and they were forced to take shelter in an abandoned log cabin. While there, they made love in front of the fire place. Suddenly, the roof collapsed and a huge beam fell on Lucas's leg, trapping him and threatening his life. Determined to find help, Sami ventured out to the main road where she flagged down a car. The driver of the car was E.J. DiMera. He agreed to help Sami move the beam off Lucas in exchange for sex. Sami slept with E.J. in exchange for his help in saving Lucas's life. In early 2007, Sami Brady learned that she was pregnant with twins setting up a "who's the daddy" storyline.

Johnny DiMera was born to Sami Brady and Lucas Horton on October 23, 2007. Marlena delivered Johnny and his sister Ali in the bedroom of the penthouse. After many fake and real paternity tests, Sami learned that Lucas was Allie's father and E.J. was Johnny's father. Sami committed to raise the twins together and refused to separate them, regardless of their separate fathers.

E.J. sided with Sami against Stefano and did not allow Stefano to spend alone time with Johnny. E.J., who by then had fallen out of favor with Stefano, refuses to let Stefano turn Johnny into the next "DiMera soldier". Despite Sami's feelings (both love and hate) for E.J., Sami allowed E.J. to be an active part of his son's life, even moved in with E.J. to get his help raising the twins while Lucas was in jail.

When Stefano went into a coma his lawyer divides up the DiMera estate. New DiMera, John Black, assumed control over the empire. However baby Johnny, who was the only remaining direct descendant of Stefano in good favor, was set up with a large trust fund, which he would receive on his 21st birthday.

Johnny remained at the center of his feuding parents, each wanting sole custody of Johnny. In December of 2010, Sami and E.J. put their differences aside to be there for Johnny when he was diagnosed with ocular cancer. The doctors caught it before it spread, but Johnny's right eye had to be replaced with a glass eye.