The movie opens with a scene of Gotham City and a news report. We got Vicki Vale reporting the latest events seen in Public Enemies, as the meteor Kryptonite shower and the leftovers of the debris have moved beyond Earths orbit.
The story continues as we see what believed to be a meteor coming down near Gothams harbor. The Dark Knight makes his appearance and as the world greatest detective, he goes in for an investigation. During his investigation, he comes across a space ship with Kryptonian letter written on it, surrounded by a handful of glowing green stones. A female appears to come out of the waters, climbing herself on Batman's Batboat. Accidentally activating it, the engines go online and the Batboat explodes by the harbors docks.
The female seems to be approaching a couple of guys in the back of an alley. The guys start teasing her when a foreign language is spoken, believed by the alley guys to be Swedish. It's actually Kryptonese. The girl attacks the guys while they approach her, whilst one of the guys is offering his coat. Running away, Batman appears in the alley. Wandering all around Gotham streets, she's surrounded by police men. While her eyes seem to be burning, heat vision is being set on, making one of the police cars explode. Escaping the police, she takes a leap on a car and while she seems to be hovering, police men fire at her. At her surprise, she finds Batman on top of a building. After attacking him, she flies away towards one of GCPD's aircraft, causing a big explosion. The Man of Steel appears to save the moment, stopping the aircraft from causing any accidents by throwing it away into Gotham City's harbor waters.
The girl all lonely crying by the floor of an abandoned building is approached by Batman, when he takes out a Kryptonite rock and powers her down. We follow Batman into the Batcave, with the girl strapped down, being examined by Batman's high-technology equipment. It appears that her DNA is not human. All of a sudden, releasing herself from the chains, she blasts off her heat vision towards Batman. Superman appears to be calming her down by speaking the same language with her. It is then revealed that the girl is Kara Zor-El, Superman's cousin from Krypton.
The movie continues with Superman and Batman in the Fortress of Solitude, examining Kara's space ship. On it, it is written with Kryptonian letters, "This vessel contains my daughter Kara Zor-El from the now dead planet krypton. Treat her as you would your own child, she would prove a treasure for your world ". Batman making sure the translation was not wrong, warns Superman that her structure is different from his, and she might be stronger than him. Kara then breaks down the door of the room Superman and Batman were in, flying scared behind them. It is Krypto that was chasing Kara. Superman then calms Krypto down while Batman is insecure of Kara's sudden appearance, and that she might be dangerous having no control over her powers. Clark confesses that she may be the only blood relative he has left, and he should not worry.
Kara is walking herself around the Hall of Krypton while trying to reason with Batman spying on her and why he doesn't like her. She then tells him a story from her youth. Jor-El, being like a father to her, and Lara Lor-Van, both believed that the planet Krypton was doomed, which is why her father, Zor-El, built also a ship with the navigation system locked on Earth, and that him and her mother would soon follow. She saw them die, followed by an awful blistering light. After those events, all she remembered was darkness and how the asteroid carried her across Earth and landed on Gotham. Batman asks her if she remembers her mothers name which she does not. Batman tells her that her cousin, Kal-El, has a lot of enemies who would do anything to destroy him and she might unintentionally hurt him. Kara leaves by saying to him that she thought she sensed him before because of his heart beat but she was wrong. She tells him that he has no heart.
The movie continues as we are transferred into the deep pits of Apokolips. We see Granny Goodness talking to a female , addressing her as one of the finest warriors of Apokolips. The test that will prove her loyalty alongside mighty Darkseid is set as Granny Goodness calls in the Furies against her. Stompa, Lashina, Mad Harriet and Gilotina make their appearance. While the female warrior lays down dead after the battle, Darkseid sneaks into Granny Goodness, expressing his disappointment. He then orders her to bring him the girl that fell out of the sky or it will be her the Furies will face next. Time sets back to Earth as we see Harbinger envisioning Kara's death.
We see Clark and Kara walking around Metropolis with her expressing her feelings of how much more she likes Metropolis over the Fortress of Solitude. Clark tries to teach her as much as possible of what it is like to be an Earth girl by taking her shopping. Later on, walking through Metropolis' parks, Clark explains to Kara that Bruce is not that bad once she gets to know him, and that adapting to a new culture is difficult. Clark also explains to her about his secret identity and the reason for wearing glasses; that being the importance for Superheroes keeping their identity secret. While Kara realizes how the world sees her cousin, by seeing the Superman statue, she feels it's a responsibility that frightens her and she doesn't want to be anybody's champion. Clark and Kara are suddenly attacked. Superman tries to save her when he realizes it's Wonder Woman and the Amazons trying to capture Kara for her own good and to teach her how to use her super powers with responsibility. Batman tells Superman that there's also another reason behind this.
Paradise Island, the home of the Amazons. While Harbinger is summoned for the battle of Kara and Artemis, she is once again experiencing visions of Kara's death. Superman tells Batman that he can't understand the point of everything that's happening when Wonder Woman takes place by telling him that there is a difference between having a power and how to use it. Kara seems to be loosing the battle when Superman intervenes by stopping Artemis, with Kara explaining to him that she wasn't going to hurt her. Superman tries to reason with Wonder Woman and Kara that she needs to get back to Metropolis and see what the rest of the world has to offer her. Superman expresses his fear about the visions Harbinger is having, when Batman turns against him on how he's let his guard down since Kara showed up. Kara flies away with Harbinger, while they discuss about their lives, and that she can always seek for Wonder Woman's help, like Harbinger did.
While Wonder Woman explains to Superman that Paradise Island is the better place for Kara at that moment, a Boom Tube appears with Doomsday coming out of it. To their surprise, the tube isn't closing and more Doomsday clones come out if it. It is then when Superman realizes it is Darkseid's plan, and that he had replicated Doomsday. Amazons are summoned and a big battle scene follows. Wonder Woman realizes that the monsters are not spilling any blood, meaning they are not alive. Superman orders Wonder Woman and the Amazon to step back and with a super blast of heat vision destroys the army of Doomsday's. During the battle Batman is the one who realizes that this whole attack was a distraction and the main target was Kara. Superman discovers a lifeless body in the sea, believing it to be Kara. It is revealed that the body is Lyla, Harbinger. It's then when the Trinity team makes the decision to go to Apokolips and face Darkseid. A small scene on Apokolips follows where Kara gets imprisoned while Darkseid tries to show her the benefits of being the captain of the Furies and the power she will be able to uphold.
Back to Earth. Superman and Wonder Woman drop by Big Barda's house. Batman already inside her house mentions that she already defeated Darkseid before. Asking for her help, Barda tells them that Kara is already lost and will be manipulated by Darkseid, like he did with her. Finally convinced to help them, Big Barda suits up and is willing to join them. Everyone seems to disagree with her decision but it turns out it is the only way as Big Barda had experience with Apokolips and Darkseid. A Boom Tube is activated and Superman, Batman, Wonder Woman and Big Barda find themselves on the grounds of Apokolips.
The first move against them is engaged by the Parademons. After they are being defeated (the Parademons), the team splits up. Wonder Woman and Big Barda follow the low road through the sewers when Big Barda mentions what a great inspiration Wonder Woman is to her. Granny Goodness shows up with the Furies and the battle begins. After a long battle, Big Barda is captured. Granny Goodness forces Wonder Woman to surrender herself when Big Barda says she would rather sacrifice herself instead. Getting herself released with the help of Wonder Woman, they defeat the Furies and capture Granny Goodness. At the same time Batman is attacked by the Demon Dogs. Defeating them, he finds himself in a room full of Hellspores when he realizes their power is enough to destroy the planets core. Superman reaches Darkseid's throne, demanding Kara to leave back home with him. Kara already having been brainwashed attacks her cousin by telling him she doesn't want to leave, when after Darkseid orders her to kill him. Superman eventually decides to fight back, trying to explain to Kara that Darkseid is using her and that she won't be free even if she kills him. In turn, Batman faces Darkseid. After telling him the code and that he reprogrammed his Hellspores, convincing him that he is not bluffing, Darkseid attacks him but it's not long after that he realizes that Batman is his only hope of deactivating the Hellspores preventing the planets destruction. Darkseid releases Kara by telling Batman that if it weren't for his plan, all would be lost.
Kara wakes up back in Paradise Island, realizing the loss of her friend Lyla. Superman explains to her the way Darkseid works, by breaking people's spirit. Kara, standing in front of Lyla's monument, opens up her heart and promises that she will not disappoint her. Before leaving Paradise Island she tells Batman her mother's name and that she now remembers. Clark with Kara drive back to Smallville where he wants her to meet his parents. Little did they know, Darkseid had been expecting them inside the Kents house. Blasting his omega beems towards Superman, Kara jumps in to save her cousin. A great battle follows with Kara and Darkseid. Superman regains his consciousness after Darkseids beating, facing him one last time before throwing him inside a Boom Tube and back to Apokolips. Kara then tells him that she reconfigured the Mother Box and Darkseid was sent floating in space where will no longer be a threat. With the battle having come to an end, the Kent family arrives only to find a place that looks like a war field.
Back to Paradise Island, everyone is gathered around, while Superman is giving a speech. He then takes the liberty to re-introduce his cousin, Kara Zor-El, or as the world would come to know her, Supergirl.