Season One of the series starts with a teenage Clark Kent discovering he's an alien. He tries to keep it secret but it soon goes public after he saves a school bus that fell into the river. When the military wants to contain him, Clark accidentally activates a defence system in the pod that brought him there, causing his powers to reach "full Kryptonian potential". The Season follows Clark attempting to find out more about his species while hiding from the military, which has supressed the knowledge that aliens exist. However, Clark's activities attract the attention of one Lex Luthor, who seeks to either destryo the Man of Steel or clone him and make a fortune on the black market. Lex prefers to do the other and so creates supervillains as distractions to allow him to study Superman's abilities. Luthor later desides to send a Lexbot to acquire a sample of Kryptonite, which Superman was revealed to be vulnerable to, pretending it has gone rogue. Although the Lexbot is destroyed, Lex manages to synthesise several forms of Kryptonite that he attempts to use to clone Superman.
In Season 2 Luthor is known to Superman as a villain but has gone into hiding. while searching for him, Superman activates a device that allows General Zod to escape out of the Phantom Zone. Zod plans to invade Earth and turn it into a new Krypton. While fighting Zod's attempts to invade Earth, Superman's existance is confirmed to the public. Also, the Super-Family begins when Supergirl and the original Nightwing and Flamebird escape the Phantom Zone. The Season ends in Superman defeating both Zod and the corrupt military force, which is replaced with a more righteous one, in the Battle of Metropolis. Brainiac is also featured.
In Season 3, Krypton's last city - Kandor - becomes a satellite orbiting the Sun staying opposite Earth in the Solar System. However, Luthor resurfaces and begins to sow mistrust between the two worlds causing Superman to prevent a war between the planets (Kandor has been fitted with a device that allows it to attract space junk to form a new planet) on several occasions. while Superman is keeping peace, Supergirl protects Earth while Nightwing and Flamebird protect Kandor. Eventually however, war does break out.
Earth and New Krypton have both suffered in the Second Solar War, so the series opens with Superman trying to fix the damage while Supergirl mourns the death of Nightwing and Flamebird. Both planets have learned to trust each other, but Luthor has managed to escape incarceration by claiming to have been mind-controlled by Zod, who returned in the Season 3 finale. Superman attempts to expose Lex Luthor's true intentions but ends up finding a secret facility called Project Hercules, which is aimed at creating a successful clone of Superman. The original clones, however, were both deformed and insane - Bizzaro clones - and so were put into hybernation. But when Zod returned in Season 3, he opened a gateway into another dimension which allowed an inhabitant of that dimension to escape and set the clones free. Although Superman tricks the inhabitant (Mxyzptlk) into banishing himself to the Phantom Zone for all eternity, the clones are more than a match for Superman. Eventually, he defeats them but by then, Luthor has infused himself with Kryptonian DNA and destroyed Superman's reputation by corrupting the hero with Red K. Superman returns to normal only to find that he has been replaced by Overman (actually Luthor). In the end, Overman's agenda is exposed and the villain is stripped of his powers. Amazon Queen premuieres alongside this Season.