Zaltar was a Kryptonian who worked in Argo City, a section of Krypton which had been spared from the cataclysm which had doomed the rest of the world. He had been interested in the planet Earth, recreating Earth products such as trees with help of the Omegahedron, a power source which he had been using without authorization from the Argo Council. Zaltar also had constructed a spaceship to which he had planned to use to visit Earth. Zaltar also had an apprentice named Kara, whom he allowed to use the Omegahedron as a reward for her completion of a Argoan school course in sixth-dimensional geometry. However, Kara created a dragonfly which had broached the Argo City shield and caused the Omegahedron to fly towards Earth, and almost killed Kara although Zaltar saved her by mending the shield with his orange sceptre. Kara then takes Zaltar's spaceship without permission to retrieve it, to the horror of her parents. Zaltar reassures them his spaceship is sturdy and she will travel to Earth unharmed, but is unsure is she can return home. As punishment for losing the Omegahedron, Zaltar exiles himself to the Phantom Zone.
Kara, now powered as Supergirl, was also exiled to the Phantom Zone, although this was due to the hexes of the villianess Selena. The banishment had weakened Kara and she fainted upon her arrival in this strange world. She was then abducted by a shadowy figure, who took her to his makeshift residence which looked like a rundown fortress. The shadowy man did not mean harm, but was rather there to nurse Kara back to health. By sheer coincidence, Kara's rescuer was shown to be Zaltar. After recovering, Kara was grateful to be reunited with her former mentor, and wondered what this prison planet was, having grown up on horror stories. Zaltar said through exploration of the Phantom Zone he has come into contact with criminals, rebels, and other neer-do-wells of Krypton. As Zaltar was of sound mind and his good outweighed his bad, he crafted his "home" of sorts and subsided on a squirt bottle of nutrition drink. Zaltar's dry sense of humor enabled him to survive such a brutal environment.
Back on Earth, without Supergirl to stop her, Selena has declared herself royalty. Kara tells Zaltar of what Selena did and said she must escape the Phantom Zone. Zaltar knows of no such way and there is no use looking, but Kara says they will do it together and he can live on Earth with her. The escape is alerted by Selena's dark magic, who sends a "cosmic whirlpool" to thwart Supergirl's return. The whirlpool nearly takes Kara, but Zaltar assures her she can escape the Phantom Zone. Zaltar pushes Kara out of harm's way, but at the cost of his own life, as he is trapped in the whirlpool. As Kara returns to Earth, she screams Zaltar's name in horror as he has died.
Despite Zaltar's death, he aids Kara one last time during the climactic fight with Selena. When Supergirl thinks Selena's black magic is too powerful and she cannot stop her, she hears Zaltar protesting that she can stop Selena.