Reviving The Lost Souls
He and his boss Jerome Valeska plot in his office to revive a group of superhuman terrorists named The Lost Souls. Then, Jerome pays him, and tells him to be ware of Bruce Wayne, and kill him if he can. After several houses were bombed, Lex in court then claimed responsibility for the mess, and told the court he can fix it. He then goes at night in a UFO to bomb the Arkham Asylum. It was revealed on a document which Gordon found on the street floor that it was part of a plan to revive dead people and turn their souls into lost souls, thus turning the human into a terrorist from the Lost Soul organization.
He then helps Jerome bomb Gotham's City Hall.
After that, Jerome enters his factory, and encounters him, thus asking him how the lost souls are doing. Lex replied that they needsome more crystal operations to become all powerful.
He later sues James Gordon for trying to destroy Lexcorp's business. He and James argue in court, and the judge tells them to stop the fight.
He then secretly reveals his team of scientists a spaceship he owns, called The X-Flight. One scientist tells the rest that The X-Flight can destroy a city in a few strikes.
Forming an alliance with Nygma
He later sat with Edward Nygma in his own office, to make a plan which will help them rule Gotham. Lex showed Nygma his plan for The XBomb, and Edward then showed him fatonium in a jar, able to use a person's fate. Lex Luthor then agreed to form an alliance with him. Luthor later used his spaceship to attack Gotham City, and destroyed tall buildings inside the city. That was to help The Court of Owls to take over the city. He later helped Leopald Otrix build the XBomb, but asked him for returns in the middle of the operation. Leopald betrayed him, pointing a gun on his head, and stating he has the right to live and no more then that. Before Leopald could shoot Lex Luthor, Nygma came from behind and stabbed Leopald with his sword, thus causing him to faint. Lex Luthor and Edward Nygma then ran away from Owlburrow (the lair of The Court of Owls) and they carried the unfinished bomb with them.
Edward Nygma later found James Gordon walking in the street and crying. Edward convinced James to save Gotham and sabotage The Court of Owls, just so Nygma can use James's fate and gain power on Gotham City instead. When Lex drove the car to Owlburrow, Nygma, who sat with James at the back, had pricked James's leg with fatonium. James yelled at him, as Nygma said it's just to give him more power and more luck. When the trio got out of the car, James fainted, as he fell on the street floor. Nygma then revealed it is fatonium, which will possibly rule his fate. Lex looked at him, but a tear fell out of his sunglasses. James later woke up, and went into the control room of Owlburrow together with Nygma and Luthor. Luthor and James shot a few guards, as Nygma had giggled proudly. Nygma then asked James to activate all bombs through the terminal computer. James had to do so, because he knew that if he fights with fate, he gets cursed. Nygma then laughed, and told Luthor to take him to the Lexcorp building. Lex Luthor, Nygma and James then entered the weapon room of the Lexcorp building. Nygma then told James to shoot Lex Luthor, and activate the XBomb which is in a room, inside the building. Lex warned him not to do it, telling him that it's not his fate. Nygma encouraged him. However, all of a sudden, James struggled with himself, thus he crawled towards Nygma. Nygma trod on his arm, however, Lex quickly took a sword and stabbed Nygma's back. As he pulled the sword out angrily, Nygma fell to the floor, but he was still alive after. Luthor then broke the helmet, which controlled the fatonium, making all fatonium in the world dissolve. James then felt tired, as Luthor gave him medicine to get up. Luthor then took James back to his (James's) home, and made sure James wakes up. James then coughed and asked him why he saved him. Lex replied that he always had a feeling things are going to change. He then left in his car, going back to the Lexcorp building. However, when he came back to his control room, Nygma wasn't there.
Last fight & Death
He later got in touch with Barbara Kean and fell in love with her. On their first date, they discussed about fighting the Court of Owls, as they both had the same intention (since Barbara also had enough of them ruining her life). They have entered a bar where Johnny was, however, he was killed by Johnny, and Barbara was forced to retreat.