Or you could use Darkseid for all 3 Movies.
JL1: Gets barely defeated at the end and sent back to Apokolips.
JL2: His presence is felt throughout the Movie, he sends agents to earth, provides criminals with weapons and tech, gathers info on the League's weaknesses. Maybe have someone manage to steal contingency plans from Batman's computer. No idea who you'd make the big bad though that the League fights.
JL3: The Movie starts early with a full assault on earth. Boom tubes open across the globe, at key locations, the military is crippled within hours and the League Members get strategically taken out, like in Justice League: Doom and Superman is taken prisoner. Orion appears and takes the remaining League members to New Genesis, where they reveal who and what Darkseid is, and promising earth and the League their aid to defeat Darkseid.
And I want the final fight to be between Darkseid and Superman alone, while the League and the New Gods take care of his forces around the planet.
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