At the beginning Superman is suspected of blowing up a Russain Submarine from attacking the US, but it was the Aquaman and the Atlanteans - he goes by the name "Orin" here. Superman rescues a few of the soldiers and they believe him to be the attacker to the public, but obviously MOST of the US doesn't believe it. Russia reveal it as a weapon training exercise and that Superman may have been responsible. He turns himself in for questioning and he's let off pending further investigation. This general however thinks he did it.
Batman appears at the beginning chasing down Zsasz in the Batmobile because he's hijacked a van with people inside.
He fired Dick and Barbara from the team because of Jason Todd being murdered and he hasn't spoke to Dick in years.
Morgan Edge is a reformed criminal, who is now a talk show host. He has Lois on his show and he starts talking about his past and he mentions connections he had with Lex Luthor. A few days later, he's dead from an "drug overdose". Lois starts investigating Lex.
Lex meanwhile is approached by US officials about developing weapons, because they believe Superman may have become a threat to the country if it was him that destroyed the submarine, which will cause conflict between nations. They plan to assassinate him.
It's also revealed that Lex has been carrying out and creating illegal weapons and experiments for years since he was 18. He's been experimenting on Victor Stone with Cybernetics and a superpowered woman, who he doesn't know is an Amazon. She's recent
And one of the people that visted Lex, regarding Superman was....DIANA PRINCE!
A lot of the amazon women were deployed in the world to make sure peace is maintained between nations by Themyscira. But Diana wants to rescue her friend from Lex and breaks into Lexcorp in the Wonder Woman outfit and fights with Mercy and several guards. Diana gets captured and is held prisoner. Lex executes her friend right in front of her.
Superman, who is suspecting that there may be life under the ocean, is then framed by that corrupt general for the murder of the Russian soldiers on the submarine and that's when Batman gets pissed! He obsesses more over those men that had families. Bruce Wayne publicly appears and bashes Superman and vows to use his company to bring him to justice. That's when Lex spots an opportunity to bring him on his plan. Lex reveals he's going to kill Superman on orders of the US, but Bruce, obviously, doesn't like that and only wants to bring Superman to justice. Bruce is actually interviewed by Clark during this part.
Lex reveals something he and the Government scientists have been working on while experiments were being made on Zod's body. It's the Kryptonite which can weaken and potentially kill cells in the aliens if exposed to a degree.
Bruce backs out of the plan and assures Lex he won't say anything...only for Batman to steal the Kryptonite bombs from LexCorp!
He heads back to Gotham and calls out Superman, who has been hiding out at the Kent farm. Superman heads to Gotham and he and Batman duke it out in a huge fight in downtown Gotham. The Batmobile turns into this flying thing and they both chase eachother around the city! Batman is victorious thanks to the Kryptonite bombs. Superman is weakened and they both slug it in the streets in front of people. Although he is now convinced Superman is innocent and fights off the Government troops sent to kill Superman; Batman wanted him put in custody only. He leaves Superman at the home of his dads old doctor friend and now he himself is wanted!
Bruce and Superman have a talk in the cave and the talk of Lex becomes prominent and Clark reveals Lois Lane is suspecting him of murdering Morgan Edge.
Lex then calls Bruce back to Metroplis and starts calling him Batman! Lex says he will keep quiet about his secret if Bruce keeps hush about his. Because all will be destroyed for him if he's apprehended by the government army.
Superman then decides to investigate under the ocean, believing he can clear himself if he finds out what destroyed the submarine. Batman decides to team up with Lois to expose Lex and they both infiltrate Lexcorp. Lois eventually finds evidence to the murder of Edge and Batman finds the secret labs where he discovers Diana and Victor. Lex appears with a **** load of guards and killer machines to kill the 3 of them. Superman eventually discovers Atlantis and pleads with them to vindicate him and make themselves part of the world above. Orin reveals he is really half human which shocks the other Atlanteans, because they thought he was pure The land above was once his home and he destroyed something he thought was going to do harm to it, while the rest of them thought it was about their home. Orin steps down as King of Atlantis and hands the title to his brother. He wishes to return to the surface and serve as Arthur Curry and take full responsibility for the destruction of the submarine.
Back on the surface, Superman heads over to Lexcorp and aids Batman, Cyborg and Wonder Woman.
Lois is captured by Mercy and taken in a helicopter, where the evidence of Morgan Edge's murder is destroyed. Lex and Superman battle each other, because Lex is in this massive battle suit thing. He flies off and sets off explosives he had planted in the secret labs to destroy all evidence of his actions. Wonder Woman manages to fly! Out with Victor and Superman with Batman.
Lex starts to fly away and Batman summons the flying Batmobile and he and Superman give chase. Wonder Woman manages to rescue Lois from falling to her death.
A captured Lex tells Bruce that he's not going to reveal his identity to anyone, because knowledge is power over him and the waiting adds to the thrill. He tells Superman that he'll get away with everything, because there'll be no evidence to link him to the events and money will buy him anything. He promises he'll finish what he started and it's personal now.
In the end, Superman and Batman are vindicated. Lex has the corrupt general framed for pratically everything. Diana obtains the lasso of truth to expose the corruption of lies and is appointed the head of a new government branch involving metahumans. Bruce and Dick reconcile. Victor is given rehabilitation treatment and sees his girlfriend again after all the years he was presumed dead. Arthur is not sent to prison because surprising new evidence shows the Russian vessel was acting on orders to attack US Soil...Then...? Martain Manhunter and Green Lantern beam Superman, Batman, Wonder Woman, Aquaman, Cyborg AND Flash, who is not in costume, into this place where they tell them that Darkseid is coming to Earth to infect and conquer it with his evil and they are the only ones who can stop him!