Elias was a main suspect when Detective Carter's number came in from the Machine. It was revealed he was indirectly involved by hiring her confidential [[informant]] to complete the hit. Elias left a vase of flowers on Carter's desk with a message mourning her loss and stole a file marked Elias from her desk.ref
Carl Elias resurfaced after Reese called him using a phone left in a trash can by Anthony "Scarface" Marconi who was impersonating a police officer.ref
Upon his father's release from prison, Elias ordered some of his men to kidnap his father. His plan failed when Carter and Reese intervened and took Moretti into protective custody. Reese later called Elias, requesting his help to find a child kidnapped by an Eastern European gang. Elias agreed to help but threatened the child himself once Reese had found her. Reese was forced to give up Moretti's location in exchange for the child's life, and Elias let them both go. Although Reese tried to save Moretti, Elias succeeded in capturing his father.ref
Elias's plan to unite the five families required him to kill the five Dons. He recruited , a [[cabal]] of corrupt cops, and used them to help him take down the Dons. After killing one Don with a car bomb planted by Scarface and gunning one Don down in front of Carter, Detectives Carter and Fusco took the remaining three into protective custody, barely escaping Elias's men. Elias then personally went to where they were hiding out with some HR cops and ordered the kidnapping of Taylor Carter. He was unaware however, that Harold Finch had shown Officer Simmons, an HR cop, photos of Elias's men watching the families of HR cops. The HR cops severed their ties with Elias and several clean police officers came to the hideout. Carl Elias was forced to surrender.