I agree that the Justice League should have to fight Darkseid in the movie but I’d do it a little differently. It would have to be after Batman’s third movie and Superman 2, Wonder Woman, Aquaman, Green Lantern and the Flash would be made.
Because of the recent surge of costumed metahumans in the world, Batman has developed a satellite through Wayne Corp to keep track of them all. Meanwhile Superman is flying around in Metropolis and hears a loud thunderous noise. He flies to it and finds a man dressed in high tech weaponry covered in battle scars, Mr. Miracle. He tells Superman that a great evil is coming to Earth, Darkseid. Miracle tells Superman how Darkseid has an army with the potential to destroy the Earth as he’s searching for the Anti-Life equation. Superman tells Lois Lane to print Miracle’s story and the world goes into panic. As Darkseid’s forces first arrive Superman, Mr. Miracle and the military try to fight him back but he’s beaten down by his forces and captured. Meanwhile Batman has been viewing the conflict in Gotham and decides to put his plan into action. It goes through a sequence where Batman recruits Wonder Woman, Flash and GL who are all public heroes. He also recruits Waynetech scientist Ray Palmer, Carter Hall, who has been outfitted with Waynetech anti-gravity wings, former criminal Eel O’Brien, vigilante Oliver Queen and Zatanna Zatara, who was the daughter of one of Bruce’s teachers. Batman takes his team and storms Darkseid’s facilities. They fight back Darkseid’s generals Granny Goodness, the Female Furies and Kalibak. They release Superman and Miracle and go to Darkseid’s main control room only to find a green alien in a stasis tube. They release him and he tells them he’s J’onn J’onzz, the last Martian. J’onzz tells them that millennia ago Darkseid captured him and forced him to find the Anti-Life equation with his uniquely telepathic mind or else he would destroy Mars. J’onnz knew that the Anti-Life equation was on Earth so he steered him across the universe for years. When Darkseid revealed he had killed all of the Martians, J’onnz was so overcome with grief that Desaad could finally get the information from his head. J’onzz tells them that it’s located in Atlantis and that’s where Darkseid is. They go to the Bermuda Triangle and see Aquaman trapped in some moisture draining containment field. Aquaman agrees to help them take down Darkseid in order to save Atlantis. They fight Darkseid in Atlantis where he finds that Aquaman’s ancestors had moved the Anti-Life Equation to the Source Wall, where Darkseid could never find it. Angered, Darkseid boom tubes the team to Metropolis so the world can see him murder their greatest heroes. As the Parademons attack Metropolis, the heroes fight Darkseid to a standstill. As it looks like he’s about to kill Mr. Miracle, he tells him he’s finally gotten his Mother Box to work and has informed New Genesis to attack. Hundreds of New Gods attack the Parademons while Superman, J’onn J’onzz and Green Lantern shoot Darkseid into outer space where they have a huge battle. With his ring, GL tells Darkseid that he’s gathered too many enemies in his time, and the entire Green Lantern Corps come and stop Darkseid. The Corps then take him back to Oa to be jailed. Back on Earth, Highfather tells Superman and the rest of the league that New Genesis couldn’t interfere until they were certain Darkseid had attacked a New Genisian. Since Miracle let himself be punished by Darkseid, the pact was broken. Six months later, Superman tells the other heroes that none of them could have defeated Darkseid on their own. In the new satellite that Bruce Wayne is financing, Superman, Wonder Woman, the Flash, Green Lantern, Zatanna, Green Arrow, Plastic Man, the Atom, and Hawkman form the Justice League. They ask Mr. Miracle to join but he says that his work on Earth is done and he just wants to spend time with his wife Barda. Aquaman and Batman tell them that they will provide help if the League needs it. Superman asks J’onn if he wants to join the team. He tells Superman that he’s all alone in the universe and that his family is dead. Superman tells him that he can have a new family on Earth with the JLA. J’onn agrees and the Justice League is formed. It shows at the end Oa, where Darkseid is being held. It shows him in a huge containment field where he says, “I’ve been in worse than this, and I’ve gotten out.” Just like in Infinite Crisis, but with Superboy saying it. After the credits as a teaser, it would show Lex Luthor sitting in jail when someone tells him about Superman forming a super team. Luthor just says to himself, “Well if Superman has one, I’ll just have to get one for myself.”
The second movie could predominantly involve the White Martians and Starro trying to conquer the Earth and the third one would be Luthor’s Secret Society and Darkseid retuning. It has a lot of problems in it but that would be the ideal Justice League movie for me.