The group of heroes part ways with Bruce. He gives them each a special radio to contact them in case they are needed. Diana queries about the whereabouts of Victor Stone. Bruce answers he tried to find him and his father Silas Stone, but was unable to. He adds that his last known contact was a Morgan Edge. Diana tells him to contact her if he hears anything else. She kisses him on the cheek before parting ways. On his way home, Bruce calls home to tell Alfred he is on his way, but there is no answer. Then he tries calling Alfred with his communicator, but still no answer. He then tries to call Barbra to apologize only to get her voicemail.
In Smallville, Martha leaves a flower shop and heads to a familiar cornfield to visit the grave of her son. When she arrives, she sees a rather large hole in its spot. She drops the flowers she had planned to put on it as she looks around for an answer to what happened.
Lois comes back to her apartment after running errands. While checking the mail, she notices someone has been through her paperwork on Mannheim. Suddenly a bag is placed over her head as two men attempt to kidnap her. She fights back, but is ultimately overtaken by the men.
Back at his lake house, Bruce looks around and sees Alfred has indeed left. He turns on the news and sees someone has desecrated Superman's grave in D.C. with scorch marks saying 'He Lives'. Then a story about Lex Luthor's release and his involvement in a military project are shown. Bruce becomes suspicious and decides to investigate.
Lois is brought into a room where a lone desk sits. The bag is pulled off her head and she sees two men sitting in the room, Morgan Edge and Bruno Mannheim. They dismiss her kidnappers as they begin to speak. Mannheim asks if she's doing well. Lois responds by demanding where she is and why she was brought here. Edge tells her that she shouldn't have gotten involved, and they can't tell her where she is. Mannheim then says they can tell why she's there. Edge reveals to Lois that they belong to a doomsday cult, founded after a strange object was collected in Roswell, New Mexico. The cult had members with high political and government positions who tried to reverse engineer the object to improve Earth's technology. The object was dubbed the Mother Box. Once they figured out how the device worked, it projected a message of an alien planet with the visage of its ruler, a stone faced man with glowing red eyes and an omega symbol adorned on his robes. The cult wanted to learn more and planned to summon this ruler to Earth. Mannheim explains that they believed that the Mother Box chose Earth as a sign that their planet was chosen for this alien race to make contact. Lois wonders why they're telling her this. Mannheim answers by grabbing her face and telling her cause she wanted to know. The pair are interrupted by a phone call from Edge's phone.
As the machine is being finished, the president, the cabinet, and military personnel are summoned to see the finished product. Among them is Secretary Swanwick who leaves for the restroom. One of them is on the phone, wearing a ring with an omega symbol. Waller says the scientists and technicians have looked over his machine to prove it is legitimate. She exclaims her surprise at how good he's been. Lex smiles and tells Waller that they will begin a weapon test, immediately. Waller asks why so soon. Lex ominously answers that the threat will be here very soon.
Edge hangs up the phone and apologizes to Lois for cutting their meeting short. Mannheim calls for his men to come back into the room. They bring in a man with a bag over his head. When they pull the sack off, the man is revealed to be Silas Stone. Mannheim tells Lois that he is a compassionate man and pulls out an egg timer. He sets it for five minutes. He orders his men to kill them, all of them after he leaves, gesturing to Stone, Lois, and Edge. Edge panics and asks Mannheim what he's doing. Mannheim talks down to him asking who's in charge here. Edge argues that he is the leader of this group, but Mannheim interjects that it was nothing more than a cult until he came in an turned it into the criminal empire it is now. Edge tries to argue once more, but Mannheim pulls out a gun and shoots him.
Lex Luthor starts to speak as they ready to unveil his new weapon. As he washes his face, Swanwick notices something in the mirror and then his face contorts into terror. Lex unveils his weapon to the crowd explaining how it works.
Lois talks to Stone as the timer counts down to less than two minutes. Lois asks him why he was there. He tells her that he was one of the scientists tasked to reverse engineer the Mother Box and see its technological advantages for human applications. He finishes by saying his son was the last experiment. Lois stares at him confused as the timer gets down to less than one minute.
Swanwick returns to his seat. Shortly after, a gun is shot causing everyone to cower in fear causing Waller to drop the remote. Swanwick tries to calm everyone down. Mannheim and bodyguards with automatic firearms have infiltrated the event.
The timer starts to ring and the men aim the barrels of their guns behind Lois and Stone's heads. As they begin to fire, the lights in the room start to flicker with creaking noises heard around the room. As the lights flicker, a figure appears behind them and attacks. Lois turns to see Batman standing.
Mannheim calms the crowd down and tells them that he plans to commandeer this weapon with one of his own. He signals his men to bring someone in. Suddenly a single, glowing red light is shone.
As they leave the building, Stone tells Batman that Mannheim is planning something huge at the event. Batman pulls out a communicator and presses a button. Lois asks him what he is doing. Batman responds calling for help. Lois wants to come with him. Batman starts to argue before Lois stops him by saying she is going. He relents. Before they go, Stone quickly tells them he has his son.
The weapon is revealed to be a human with cybernetics covering most of his body with an arm cannon. Mannheim calls him Cyborg. Cyborg doesn't look too pleased to be there. Mannheim whispers to him if he does what they ask, his father will stay alive. He orders Luthor to start the machine.
Batman rushes to the event in the Batmobile with Lois in tow, meeting with the others to stop Mannheim at the event. They rush through traffic and try to make it across a vertical-lift bridge as its lifting. The gap is too far even for the Batmobile, so Batman tries to call Alfred for the Batplane. No one answers. Batman keeps calling, despite knowing that Alfred is no longer there. He ejects Lois and himself into the air and suddenly the Batplane appears to catch them. Bruce quickly thanks Alfred, only to hear a woman's voice. Barbra takes the thank you instead citing she got his message. Batman pilots the plane to the event with Lois.
At the event, the machine starts up, smashing atoms. Mannheim then tells the crowd to kneel to their new master and orders his men to kill the ones who resist. One general refuses and one of his bodyguards aims their gun, ready to squeeze the trigger until a device with a beeping red light is attached to it. More devices appear, attaching themselves onto the guns rendering them useless. A red blur and small lightning bolts then come knocking out the henchmen, and a golden lasso wraps around Mannheim tying him up. Batman, Wonder Woman, The Flash, and Aquaman appear with Lois checking on the former hostages. Suddenly loud clapping is heard.
Luthor stands up with a huge, Cheshire grin on his face. He congratulates Bruce on finding the others and getting them to commit. Barry looks confused at Luthor and asks him what he is talking about. Bruce reveals that Lex planned the whole thing. Lex nods along, feigning astonishment at what Batman is saying. Bruce tries to continue, but Lex interrupts by saying he's the magician and only he gets to spoil the secret. He reveals that he had ties to Mannheim's group the entire time, and that's how he learned about Dr. Stone's research and Cyborg's existence. He then reveals the cannon is actually an insert for Cyborg's cannon, and the weapon isn't a weapon at all. Diana interjects that he plans to summon a black hole. Luthor says she's correct, but adds one that he can control. He plans to summon his threat to Earth by creating a boom tube with the Mother Box technology in Cyborg. Waller then claims 'well I'll be dipped'. The particle accelerator starts becoming louder, signaling Luthor to Cyborg. Luthor tells Cyborg its time for his cue unless he wants to see his father again. Cyborg hesitates as he slowly places his cannon to the insert. Bruce tries to tell Cyborg that his father is safe, but can no longer be heard over the roar of the machine. He puts his cannon in and it activates. A large portal is summoned to Lex's delight.
Cyborg hears a voice saying his father's fine in his head. He tries to stop the machine, but he can't get his cannon freed. Debris and chairs start getting vacuumed into the boom tube as Cyborg struggles to get free. Waller tries to grab the remote only for it to be drawn into the vortex as well. The others try to keep the audience from being sucked in. Suddenly Swanwick rises and sprints to Cyborg. Cyborg looks and sees Swanwick trying to help pull his cannon free, phasing through the insert as Swanwick slowly changes shape, revealing a green form. The boom tube becomes unstable and slowly starts building suction, taking the entire building with it. Lex is about to be sucked in its vacuum before being saved by Batman and Wonder Woman. The green man helps get Cyborg away from the hole. Lois starts losing her grip as the hole becomes too strong, she slips and screams.
Suddenly a loud, roaring is heard like thunder. Lois is caught by a familiar pair of arms in a partially blue and black suit. She looks up to see Clark. Clark smiles at her and quickly gets her away from the black hole as he's the only one strong enough to escape its vacuum. He then tries to use his heat vision to destroy the machine causing the black hole to collapse. A large boom is heard and light escapes from it, leaving a crater where it once stood. Lois quickly runs up to him and he picks her up. She quickly kisses him, claiming she always knew he'd come back to save her.
Lex and Mannheim are arrested for their crimes with Waller making sure they get the worst of it in Belle Reve. Cyborg quickly thanks the green man for helping him. The man reveals his name is J'onn J'onnz. Feeling out of place amongst the others, he quickly changes his clothing to better suit theirs. He comments to Superman that he's looking well, hinting he was the one who resurrected Clark. Quickly the press arrive, Batman, who doesn't like to handle the press, tries to leave. Superman stops him, claiming he will handle it. Superman talks to the press with the other heroes surrounding him. He tells the public that they are here to protect them. He beseeches that all metahumans come out of hiding and join their crusade of justice.
As Lex is being incarcerated, Waller and the real Swanwick have a conversation. Swanwick asks her how they plan to defend themselves against the threat, frightened that something has been contacted. Waller says they already have a weapon, referring to Superman and the others.
Lois revisits Arkham Asylum to see Toyman. She reveals to Toyman that she dug into Mannheim's financial records and found that he loaned money to his father, Lazlo. Toyman seems phased by this. She adds that his father couldn't return the money, so Mannheim had him killed. Toyman confirms Lois's theory and tells her that Mannheim took his father, and his childhood with him. He reveals that's why he kills children, not out of hatred, but of envy. He sees their happiness and longs for those days as well. He then tells Lois where the bodies are buried.
Bruce returns home to see Alfred making dinner. When he asks what he was doing here, Alfred answers you can thank Ms. Barbra for convincing him to stay. Bruce smiles as Barbra appears, telling him she would like to come back, becoming Oracle.
The ending is a montage of Metropolis police finding Jason's body with Lois and Cat, Lois and Clark returning to the Planet, Cyborg watching football with his dad, Barry visiting his mother's grave, Aquaman helping prevent an oil spill, Diana seeing her mother, Barbra, Alfred, and Bruce sitting down to dinner, and Clark returning home to a crying Martha with J'onn in tow. All with Lex narrating a monologue, 'twoeth by land, oneth by sea, oneth man, and then there's three from the heavens above. The bell tolls for thee.' A final shot is shown of a familiar pinging sound as a voice is heard telling someone they traced the boom tube's location to a distant planet. An alien with a stone face and glowing red eyes appears and smiles.