He is first seen in the episode Targets where he is called in to act as an arbitrator between the two states North- and South Rhelasia who are on the brink of war. The negotiations are taking place at a hotel in Taipei but when Luthor arrives he is almost assassinated by the hired killer Cheshire. After Cheshire is stopped with help from Red Arrow, Luthor vouches for Red Arrow who has mistakenly captured by the police. Roy is not convinced by this act of nobleness and calls out Luthor. Luthor replies that while he does not claim to be an angel, this time he is on the side of the angels. He then heads inside the hotel. Inside the hotel, Roy talks to Luthor again, revealing that he knows that LexCorp is selling weapons to both Rhelasias and would thus profit from war. Luthor assures Roy that there would be much more profit in investing in a peaceful Rhelasia and implies that he may not have been the target of the assassin at all. Luthor attempts to hire Roy to investigate the assassination attempt. While Roy decides to investigate, he claims that he won't do so for Luthor.
After investigating, Roy returns to Lex to reveal that it is Ra's al Ghul himself who wants Lex dead.
During the peace summit, Cheshire once more attempts to assassinate Luthor and the leaders. Everyone present is saved by Red Arrow and Aquaman who shields the people with an aquatic sphere. The arrival of more League assassins, including Sportsmaster, causes both Rhelasian leaders to retreat to the dais. Luthor remains in the room, watching the fight. When one of the assassins jumps onto the dais, Luthor's assistant Mercy Graves is reveled to be an android who shoots the assassin out of the air. This demonstration of power compared with Luthor saving both their lives convinces the two leaders to sign a peace treaty.
After everything is well and Red Arrow and Aqualad have returned home, Luthor meets with Ra's al Gul. It is made clear that both deviced a scheme which would result in Rhelasia's unification under LexCorps political and economical guideance. Both toast to each other, revealing that they are both part of The Light.
On Thanksgiving, Luthor contacts Superboy and invites him to Washington D.C.. There, he introduces himself and reveals to him that he is the new chairman of the board for Project Cadmus. He tells Superboy that Cadmus has built another super clone. Outraged, Superboy heads to Cadmus but at first cannot find any evidence for the clone. Meanwhile, Luthor watches surveillance footage of Superboy examining the facility. Just as Luthor had anticipated, Superboy eventually finds the new clone and releases him. He is promptly attacked when the clone sees the Superman sigil on his shirt. Luthor seems to be concerned when Superboy is beaten.
Luthor then contacts Superboy once more, revealing to him that when he was created, he was created by kryptonian DNA mixed with human DNA opposed to the new genomorph who is purely krypton. Luthor provides Superboy with devices called 'shields' which supress his human DNA and allows him to use his powers at full capacity. Superboy later finds out that Luthor is the founder of Cadmus Labs.
After Superboy fought the genomorph he angrily confronts Luthor for using him. Luthor had planted a tracker on the shield box to find the missing genomorphs (who had secretly built an underground city in order to be free). Luthor does not deny it and also reveals to Superboy that the human DNA used to create him was Luthor's DNA. Luthor claims to be a better father than Superman ever was to him. He tells Superboy that while Superman sees the world as black and white, Luthor sees it as shades of grey. Superboy angrily offers him back the shields, claiming that he doesn't want them. By using a code phrase, Luthor then shuts down Superboy. When Superboy awakens, it is late night and Luthor is long gone.
After having obtained influence over Young Justice team members Superboy, Miss Martian and Artemis, the Light decides to use them to their advantage. Planning to bring their new assets to Santa Prisca to elaborate their plans, Luthor contacts Superboy.
After Superboy has used up all his shields, Luthor claims he has more and lures Superboy to Santa Prisca. There he reveals that he has not come alone but accompanied by Queen Bee, Sportsmaster, Blockbuster and Bane. Cheshire then arrives with Artemis and Queen Bee calls in Miss Martian. Superboy approaches Luthor, feigning to join them in exchange for more shields. Luthor detects the lie and once more uses the code word on Superboy, forcing him to stand down. Before further actions can be taken, Artemis and Miss Martian turn on the Light and attack Blockbuster and Queen Bee. Luthor is approached by Superboy, revealing that the deactivation code was wiped from his brain by Miss Martian. As most of his men are defeated, Luthor calls in Bane and his soldiers to assist them. Bane's mercenaries are taken out by the rest of the Young Justice League. Luthor attempts to escape with the unconscious Queen Bee but is stopped by Aqualad. He sends Mercy Graves to take care of Aqualad and flees into the jungle. While the rest of heroes and villains fight, Luthor and Queen Bee escape via helicopter.