A brief recap shows that Superman has been brainwashed into believing he is Darkseid's adopted son. On Darkseid's orders, Superman has invaded Earth and decimated its military. Lex Luthor and General Hardcastle have used a Kryptonite Bomb to take Superman down, while Supergirl was caught in the explosion as well.
We open with the aftermath of the explosion. Lois Lane walks through the rubble, trying not to breathe in the Kryptonite dust that hangs in the air. Through the haze, she sees army soldiers carrying both Superman and Supergirl away. Superman groans, and Lois tries to help the two, but is stopped by the men. A combination of Lois's voice and the shock of the Kryptonite attack have managed to reawaken Superman's memories.
He remembers back to a mission in space over a month ago. He was inspecting a distress call from a ship floating through space. When he arrived, he was attacked by the ship's weapons and rendered unconscious. It was a trap. From there he was taken to Apokolips, where he was tortured and brainwashed until he believed that he was Darkseid's loyal son.
Superman awakens from his dream in a private jail cell. He is dressed in a prisoner's jumpsuit and is handcuffed under a red sun lamp. General Hardcastle enters and says that he must remember to thank Lex Luthor for the special lights, as Superman's powers disappear under a red sun, like that of his native planet Krypton. Hardcastle reveals that the only reason Superman is still alive is to answer the Government's questions. Superman tries to explain that he was not responsible for his actions, and asks where Supergirl is. Hardcastle doesn't believe him and leaves without answering.
At a press conference, the Press Secretary tells the reporters that the alien threat has been neutralized. The crowd begins whispering "Does that mean Superman is dead?" Lois Lane goes nuts, and shouts that Superman was still alive after the K-Bomb blast, and demands to know where he is being held. The Press Secretary leaves without answering.
Before a secret military court, Superman, still under a red lamp, is being tried as a traitor. Superman explains that it was all Darkseid's fault, but Hardcastle scoffs, saying that Superman lost his bid for control and is now just trying to pass the blame. Superman promises to do whatever it takes to make things right, and restore the world's trust in him. Hardcastle asks how he would ever manage that, considering all that has happened.
Outside, Lois uses her father's connections at the Pentagon to gain entrance to the army base where Superman is being held for interrogation. Once inside, she sees Superman being lead back to his cell. Momentarily out from under the red sun lamps, some of Superman's strength returns, and he tries to escape, but is blasted with more kryptonite dust.
When Hardcastle is alerted to Superman's escape attempt, he is furious. Lex Luthor is in the general's office, and he points out that they can't risk Superman or Supergirl escaping and regaining their powers. Lex opens a brief-case containing two hypodermic needles, each filled with liquid kryptonite. Hardcastle agrees that this is the only way.
Lex and Hardcastle enter Superman's cell brandishing the needle. Superman asks "So this is how it ends?" Lex says not to think of it as an ending, since his bio-tech team will spend years dissecting Superman's corpse to learn its secrets. Superman asks Lex one favor, since they are both at equal human levels now, under the red light, and Lex agrees. Superman punches Lex one good time and shatters his jaw. In the melee, Lois enters and blasts Hardcastle with a stun-gun. She frees Superman from his shackles and they escape.
As the alarms go off, Superman uses his returning x-ray vision to search for Supergirl and finds her. She is being held in another cell, under a red sun lamp as well. Superman manages to bust down the door, but Lois has to go into the red light and get the weakened Kara. Outside her cell, Kara tells Superman, "You have some explaining to do..." before she is shot in the chest with a laser gun. Superman weathers the blasts and takes down the guards, eventually finding an exit. Finally under direct yellow sunlight, Superman's powers return, and he tells Lois to hang on as he carries Kara. They fly away toward the city.
At STAR Labs, the scientists stabilize Kara's condition, but Professor Hamilton says that they can't help Superman or Supergirl without it being a direct act of treason. Superman grabs Hamilton by the throat and demands he save Kara. A terrified Hamilton agrees, if Superman just promises not to hurt him. Superman realizes what he is doing and puts the professor down. He asks "Please..." and walks away.
Lois finds Superman in another room, putting on a spare Superman-suit. Superman says that by the look in Hamilton's eyes, he knows no one will ever trust him again. Lois asks what really happened. Superman explains about Darkseid's brainwashing, and about how Darkseid has taken the most important things in the world from him. He tears open a vault and removes a Mother Box. He tells Lois that he is going to Apokolips the settle things once and for all. As Superman opens the Boom Tube, Lois whispers "Heaven help you..."
Superman arrives on Apokolips and is met by a wave of Parademons, which he vaporizes using his heat vision without a second thought. From a distance, Kalibak sees this and announces Superman's arrival to his father. Darkseid says to let him come.
Superman breaks into Granny Goodness's Laboratory, shouting "You're first on my list!" Granny attacks Superman, but he knocks her back into her own memory wiping machine and her brain is fried.
Outside, Superman is attack by the Furies, including Lashina, who was his lover when he lived on Apokolips. They try to stop him, but Superman flies through one of the fire-pits, burning them all off.
Superman breaks down the door to Darkseid's throne room, and dispatches with Kalibak easily. He approaches Darkseid. "You used me!"
"I told you, if you would not by my knight, then you would be my pawn," Darkseid says casually.
"At least you are a man of your word."
"I am many things, Superman. You couldn't begin to imagine half of them. But here and now, I take on the role of executioner."
Superman and Darkseid begin to battle. And Darkseid quickly gains the upper hand with the Omega Beams shooting from his eyes.
"I will give you the gift of a quick death. Infinitely more preferable to returning to Earth. There your legacy would be one of fear and distrust. Where you would be a pariah, desperately chasing the favor a world that curses your name."
Superman lifts up a piece of the floor to deflect Darkseid's blast. He takes the opportunity to begin pummeling Darkseid, who finally becomes enraged. "You dare strike me!"
"That was for Dan Turpin!" Superman shouts.
"The good man you killed!"
"If I knew one human's death would bring you such pain, I would have killed a thousand more! And I will! Take that agony with you into oblivion!" Darkseid bellows as he fires his Omega Beams again.
This time, Superman grabs Darkseid's head, blocking the blasts with his hands. The resulting backlash is so massive it destroys Darkseid's palace. Both Superman and Darkseid, clothes torn and skin bleeding rise and face each other again. But this time, Darkseid collapses at Superman's feet.
As the scared inhabitants of Apokolips watch, Superman stand from the edge of the high ruins and tosses Darkseid to the ground below. "Darkseid has been defeated. You are all free."
The people stand there a moment, and then begin to help Darkseid. They carefully and lovingly pick him up and carry him off. He holds up his hand to stop them a moment.
"I am many things," he tells Superman. "But here, I am God..." And the people carry him to safety.
Superman turns to go back and finish things, but a hand stops him. He turns to see a weakened and wounded, but still living, Kara. She begs him to not keep playing by Darkseid's rules, and says that she just wants to go home. Superman hugs her and agrees.
On the evening news, they ask the question "Superman: Friend of Foe?" A random man on the street says Superman should go back to where he came from. Professor Hamilton says that he used to call Superman a friend, but now... Jimmy Olsen says that Superman has saved the Earth dozens of times, and we should trust him. Lex Luthor says, as best he can with his jaw wired shut, that no one man should have that much power.
Superman stands atop the Daily Planet building, listening to everything that is being said in the city about him with his super hearing. Most of it bad. Lois walks up behind him and says to stop listening. Superman says that they are right, that he did lose control for a while there. And if he can't trust himself, how can he ever regain the trust of a whole planet. Lois kisses him full on the mouth, and says "One person at a time."
Superman smiles at Lois Lane and they embrace atop the Daily Planet.