On Krypton, Jor-El and Lara hurry to send their child. Before Jor-El could put his fingerprint, implanting genetic code, into Lara's egg which is in a birthing matrix, Zod interrupts them and has his men subdue Jor-El and Lara. Zod implants his genetic code into Lara's egg and sends the ship into space moments before Krypton explodes. The ship crashes on Earth in a country called Mexico. One of Luthor's men finds the ship empty and orders it to be sent to Star Labs while a Mexican couple takes the child away from the scene.
Years later, Superman, Batman, and Wonder Woman raid an armed bunker to retrieve stolen files before Trevor's men could get there. Trevor is appalled at the massacre of the terrorists by Superman's group. The next day, people protests about the terrorist embassy massacre. Superman or Hernan shares with Wonder Woman, Bekka about how they could bring the world under their influence. Silas Stone meets up with Superman. In an arctic region, a scientist name Victor Fries tries to upload files. He gets attacked by a strange intruder. The intruder captures Victor and drains him of his blood. Elsewhere, an intruder attacks a scientist named Ray Palmer who was on his way to deliver miniature horses.
Meanwhile, Will calls Kirk while Tina joins their conversations. Will tells Kirk that he has no luck with the tests on getting the cure. Will then informs Kirk about Ray Palmer's death. In a lab, Silas tests out an equipment for a request from Superman. Victor tries to ask his father about Superman. Suddenly, an intruder attacks Silas and his son. Both Silas and his son attempt to fight back, but they are wiped out by the intruder's heat beam. Next morning, Trevor and Lane visit the crime scene where Victor was incinerated. Superman finds out about the case. The Justice League debrief together where Batman informs them that they are being framed with the deaths of scientists. Superman asks Wonder Woman to contact Trevor and get in touch with him.
Later that night, Batman digs up information on the scientists and finds out they all worked under Luthor at one point. In Kirk's past, he, Will, and Tina pose for a grad photo. After Luthor's speech, Will tries to convince Kirk to attend the party tonight. Will and Tina get Kirk home where Kirk sees Will's ship in a bottle that is being build by Nanite. realizes Will's Nanites could be the key to rebuild the cell structure. At the hospital, Tina and Will stays with Kirk. During some experiments, one of the mice survives. Kirk decides to take this chance to inject Nanites into his blood despite Tina's concerns. In an alley, Kirk wonders and runs into thugs who tries to rob him. Kirk bites a man and tries to drink blood but stops.
Superman visits Lane in her office where he invites Lane into his tower. He explains that he asked Stone to help retrieve files about Krypton from the ship. Superman believes his father was doing good. Wonder Woman calls Superman about President Amanda Waller's call. Kirk visits Will to ask about Luthor's Project FairPlay. Will wouldn't answer. Tina meets with Kirk and is worried about him. Kirk reassures Tina and Tin that he would protect them. Wonder Woman visits Trevor and challenges him to get information. Trevor's words rattles Bekka about how she used to belong to someone.
In Wonder Woman's past, her father, Highfather, proposes to Darkseid, a marriage between Orion, Darkseid's son, and Bekka, his daughter. Orion takes Becca to a spot among the crystals. He presents Bekka his wedding gift, a sword that has a boombox inside of it. During the wedding, Bekka takes Orion away when Highfather's men massacres Darkseid's men. Highfather kills Orion who tries to protect his father. Bekka states she would have inform them if she had a second chance. She escapes Apokolips, refusing to take Highfather's side.
While Kirk follows Will and Tina to a meeting with a group of scientists who are associated with Project FairPlay. Help arrives too late when Kirk couldn't protect Tina who was stabbed. Superman finds Will who was burned severely but barely surviving. Kirk suggests Superman to visit Luthor. Luthor reveals the files on how Superman was conceived from cruel man named General Zod. Luthor insists that he gave him fake files to make sure Superman believes he was hero. Shortly after Superman leaves the ship and telling Luthor that he was the product of Zod and Luthor's creation, an intruder blows up Luthor's ship. This event caught by NASA had false implications on Superman being the murderer. Framed for murder, Amanda initiates FairPlay.
As Superman and Wonder Woman try to buy time and fend off Trevor's men, Tina infiltrates the tower and revives Magnus. It turns out Will Magnus is the mastermind behind the massacres of the scientists. He revealed he had killed Tina by accident after being angry at her for mentioning her concerns over Kirk. Will states he has a Nanite bomb which needs the Krypton core to power it. This will allow him to boom tube nanites in everyone's brain to control them. Luthor boom tubes in between Trevor's men and Superman & Wonder Woman to expose Will. After Superman breaks into the tower, a battle ensues. While Kirk fights with Will, Wonder Woman combats with Platinum. After Platinum and Will are defeated, Superman arrives to take the core that was about to explode and throws into space.
After the event, Lex Luthor and Wonder Woman departs for Wonder Woman's world since Wonder Woman wants to confront her past. Lex gives Superman the original files and tells him to be a real hero. Kirk helps Superman with the files to help the Earth.
- Benjamin Bratt as Hernan Guerr / Superman
- Michael C. Hall as Kirk Langstrom / Batman
- Tamara Taylor as Bekk / Wonder Woman
- Paget Brewster as Lois Lane
- C. Thomas Howell as Dr. Will Magnus
- Jason Isaacs as Lex Luthor / Metron
- Dee Bradley Baker as Ray Palmer
- Eric Bauza as Ryan Choi
- Larry Cedar as Pete Ross
- Richard Chamberlain as Highfather
- Trevor Devall as Emil Hamilton
- Dan Gilvezan as Pat Dugan
- Grey DeLisle as Tina/Platinum
- Daniel Hagen as Doctor Sivana
- Penny Johnson Jerald as President Amanda Waller
- Josh Keaton as Orion
- Arif S. Kinchen as Michael Holt
- Yuri Lowenthal as Jor-El
- Carl Lumbly as Silas Stone
- Jim Meskimen as Victor Fries
- Taylor Parks as Victor Stone
- Khary Payton as John Henry Irons
- Tahmoh Penikett as Steve Trevor
- Andrea Romano as Jean Palmer
- Andre Sogliuzzo as Cop
- Bruce Thomas as General Zod
- Lauren Tom as Lara
- Marcelo Tubert as Tough Guy
- Kari Wahlgren as Karen Beecher