Weeks after the events that led to Lex Luthor's arrest, the impeachment of his presidency, and Batman's success in saving the world from the impact of an arriving meteor, a spaceship lands in Gotham City Harbor and a young girl with no knowledge of English or any other human languages emerges. She accidentally causes all sorts of havoc with her Kryptonian-like powers until the Dark Knight exposes her to a piece of Kryptonite. With Superman's help, they discover that the girl is Kara Zor-El, the niece of Jor-El and Superman's biological cousin. While Superman welcomes Kara, teaches her English, and helps her adjust to Earth society, Batman remains suspicious. Tipped off by Batman, Wonder Woman and Lyla ambush Clark Kent and Kara in a park and take Kara to Themyscira, on the basis that only there can she learn to control her powers. Superman reluctantly agrees, but still prefers to watch to Kara himself.Meanwhile, on the planet Apokolips, Darkseid learns of Kara's presence on Earth, and orders her to be captured and brought to Apokolips as a possible candidate to lead the Female Furies since the departure of Big Barda. While Batman and Superman are checking on Kara on Themyscira, a horde of Doomsday clones arrive from Apokolips. Superman, Wonder Woman and the Amazonian army fight them for a while until Superman vaporizes all of them with a single blast of his heat vision, but Batman discovers that Kara is missing, and that Darkseids Omega Beams have killed Lyla (while trying to prevent Kara's abduction). Distraught, Superman vows to avenge her and save Kara. Batman, Superman and Wonder Woman locate and recruit Barda to help them find their way on Apokolips. Once there, Superman tears his way to Darkseid's palace while Wonder Woman and Barda go through the sewers directly into the fighting arena, where Granny Goodness and the Female Furies ambush them. After a long fight, Granny and the Furies are subdued. Batman, meanwhile, makes his way underground and finds the Hell Spores, the source of the fire pits on Apokolips, and activates them.Superman encounters Darkseid, who sets the brainwashed Kara on him. Kara pummels Superman while Darkseid watches, until Batman confronts Darkseid and informs him that he has activated the Hell Spores, all of which will destroy Apokolips. He issues Darkseid an ultimatum: free Kara and promise to leave her alone and Batman will deactivate the Spores. Intrigued, Darkseid admits his admiration for Batman's tactics. Acknowledging that neither Superman nor Wonder Woman has the "strength of character" to destroy an entire planet, Darkseid relents. Superman manages to defeat Kara and Barda and Wonder Woman present Darkseid with the subdued Granny. Defeated, Darkseid allows them to leave Apokolips.As Kara convalesces on Themyscira, she confesses to her cousin her fear that Darkseid may simply have exploited an evil inside her to have her do terrible things at his command. To that, Superman firmly dismisses that saying that Darkseid is an evil New God who lives for manipulation with numerous resources to force anyone to bend to his will and Kara thus has nothing to regret. With their lives normal again, Clark decides to take Kara to meet his adoptive parents in Smallville. However, Darkseid, who was waiting to kill Superman, ambushes them: he had promised to leave Kara alone, but not Superman or Earth. Darkseids Omega Beams blast Superman into orbit, leaving Kara to face the tyrant herself.A lengthy battle ensues with Kara (having received both Amazonian and Apokoliptian training) putting up a respectable fight, but Darkseid eventually overpowers her. Superman recovers and returns to Earth to confront Darkseid again. He gains the upper hand and pummels Darkseid using a combination of punches and heat vision at super speed. Darkseid grabs Superman and begins attacking him with Omega Beams. As Superman's skin starts to glow red hot from the assault, Kara uses Darkseid's Mother Box to activate a Boom Tube behind Darkseid. Superman uses the momentary distraction to his advantage and pushes Darkseid through. While Superman anticipates Darkseid's eventual return from Apokolips, Kara informs him that she changed the coordinates to a random spot in space, leaving Darkseid floating around frozen in ice. Having saved her cousin's life and found her place on Earth, Kara decides to use her powers to fight for altruism under the alias of Supergirl. She is met with applause by Wonder Woman, the Amazons, and, finally, Batman. Superman and Supergirl then fly off to Metropolis.