Pt. 1 would be about natural disasters around the Earth and the pre-league (Superman, Batman, Flash, Green Lantern, Aquaman, & Wonder Woman) come together to fight the natural disasters. But, at the conclusion of the movie we find out that it's actually not natural disasters, but an alien by the name of Darkseid has been causing the disasters. We find out by a visitor, Hawk Girl, the true source because her planet has already battled Darkseid and was almost destroyed. As the pre-JLA works with the government to battle Darkseid, they come to know of the whereabouts of J'onn J'onzz who was captured a year ago. He came to warn Earth about the pending attack but was captured by a Black Ops government agency known as Cadmus. Darkseid sends a broadcast to Earth about the pending attack. Batman and Superman reveal a "space station" that they have been working on with courtesy of Wayne Industry and some of the technology that Kal-El has knowledge of via The Fortress of Solitude. The movie ends with The Justice League getting to know their new headquarters.
Pt. 2 is their battle with Darkseid. Darkseid is a monumental character and should be dealt with in more than just 1 film. At the end of course, he is defeated with a little help from the "New Gods". The Justice League is officially formed.
Pt. 3 shows the planet recooperating from the attack. During this time Lex Luthor is putting together the Legion of Doom to defeat the now weakened heroes. Lex, from the blood of Superman during the 1 on 1 fight with Darkseid, has created Bizarro. Most of the heroes have been captured. The second tier heroes (Supergirl, Steel, Green Arrow, NightWing, John Stewart (who now has the ring due to Hal Jordan being beaten nearly to death) along with Batman) infiltrate, rescue the heroes, and destoys the Legion of Doom's network of world power.
Ok, that was from the top of my head, but I think it would work. Again, Darkseid is a character that should span over 2 (even 3) films a la Lord of The Rings and Harry Potter. He's a bigger than life character. I don't think 1 movie can do him Justice
woot: ).