I'd just like to say this was all lavenger's idea and he decided what sides the heroes were on.
So it all starts when trust in heroes is dwindling after the most recent dc event, maybe trinity war, to resolve the situation the government put out a American sponsors hero.
When this hero makes a grab for power of the world, a bit like injustice. This hero is confronted by the justice league. Hal, who is on the JL, kills this hero/villain.
This starts a debate amongst the government about registration. They're concerned if superman or someone on his power levels did this. Eventually the government pass registration and a dispute starts in the justice league. Hal, shazam, Barry,Wally,hawk man are all pro reg, whilst batman, Wonder Woman, aquman , green arrow, zatana and cyborg are all anti reg.
Amanda Waller goes to Gotham and stages a bank robbery to speak with batman, when Amanda tells batman about the new pro reg team, batman tells he will have nothing to do with it and escapes.
If you want to see the sides look at lavenger's list.
In Gotham villains attack the mayors office, batman intervenes when he goes into the building he finds it on fire and looks at the bodys, when he does a retina scan he learns that the body's are fake.
It's a trap! The villains who attacked were the suicide squad. Batman is confronted by the pro reg heroes and is placed under arrest. When the anti reg heroes come in, a huge battle ensures and this is when Kyle defects over to the anti reg. Amanda tells Steve to take a shot on Wonder Woman and batman but instead he tells his men to fall back, Steve and Kyle are then placed under arrest.
Batman approaches superman to join anti reg abut they are interrupted by Hal and shazam a battle between the heroes takes place and superman decides to remain neutral.
Batman then plans a prison break and kid flash defects over to anti reg. during the battle of the prison brake Barry and wally take Bart's powers away and place him in prison.
Aquaman gets the Atlantan army to join anti reg, this adds to bat mans army but during a meeting of the anti reg heroes, simon baz, who was a spy on Hals side, gets thrown through the roof. His last words before he dies are "he's gone to far". We later learn that Hal has stolen green lantern rings to boost his power and shazam has stolen Mary and Freddys power.
A huge battle ensures and Hal is about to kill batman when the neutral heroes burst in and superman takes Hal out.
The government the repel the registration and Hal, shazam, hawkman are placed under arrest.
Batman and superman are placed on a council of politicians reviewing superheroes actions.
Epilogue: Amanda Waller is debriefing the suicide squad when death stroke comes down and kills her, he tells the suicide squad that whilst this mess was going on someone was creating an army.