A/N: All right, people, this is it. I gotta finish this. Even if it will be short and unsatisfying, let's just get this over with, b/c this will be the last of it. There will not be a third part to this. This is the end. Enjoy what you can.
Following Darkseid's takeover of Earth, he begins conquering other inhabited worlds using the Mother Box, decimating civilizations and taking their survivors as slaves back on Apokolips, who are dying out in droves (this is to fulfill Darkseid's wishes to wipe out every single individual in the universe). Doomsday is used to raze the remnants of the conquered planets to desolate wastelands. Amidst all this, however, Orion has organized a growing band of rebels of various species, of which Lois and Jimmy Olsen are a part of, against Darkseid's tyranny, but it doesn't gain much ground; he loses more members that he gains to the powers of Apokolips. Meanwhile, Superman dies almost one hundred times in Darkseid's resurrection chamber (btw, I forgot to add that in this universe, red kryptonite hinders Superman's abilities to nothingness) before he wakes up from a death to find all the red kryptonite gone. With that, he is powerful enough to break free and he roams Darkseid's palace. He kills every one of his guards and frees Big Barda, which allows her to kill Granny Goodness. But they only find out that Darkseid and Jason have claimed Earth as their new home so they can lead the hunt for Orion and his rebels. Superman and Big Barda escape the palace and take the latter's spaceship to return to Earth.
Orion's group, including Lois and Jimmy, are cornered by Apokoliptian forces and are taken to be executed before Darkseid and Jason in the basement of the ruined Daily Planet. But before they can be executed, Superman and Big Barda, arriving from Apokolips, come in and swiftly take out the executioners. Darkseid and Jason manage to escape, and in their place, Doomsday returns. Doomsday manages to decimate most of Orion's rebels, leaving the likes of Lois and Jimmy alive though, but in the end, Superman and Big Barda tagteam to finally beat him into several rocky machine parts in an epic fight that sprawls throughout Metropolis. However, with most of his rebels dead from the conflict, Darkseid manages to surprise and overpower Orion, killing him out of personal spite. Jason, meanwhile, appears before Superman and Big Barda not as an enemy, but as an ally; he tells them that when he watched Superman die, he realized that he was his real father rather than Richard White, which is why he removed the red kryptonite from Darkseid's resurrection chamber. He then agrees to help them take Darkseid down; however, up in Earth's orbit, Darkseid's spy, Desaad, tells his master of Jason's treachery. Darkseid decides to return to Apokolips via the Mother Box while Earth's occupying forces take down Superman, Barda, and Jason.
While the trio of heroes (Superman, Barda, and Jason) are ambushed by Apokoliptian forces, Superman is able to fight past them to fly up into the sky where Darkseid intends to depart. He manages to catch up and tackles Darkseid through the portal, where they end up back at Apokolips in Darkseid's throne room. There, they have a final showdown which then extends out into the barren grounds of Apokolips where the slaves work and die. There, Superman ends it all by grabbing onto Darkseid and casting the both of them into a giant lava pit, where Darkseid's screams define his death. And with the death of their ruler, all of Darkseid's warriors, on both Earth and Apokolips, commit suicide, signifying the definitive end of the Apokoliptian empire and freeing the remaining slaves. Barda, however, informs Jason, Lois, and Jimmy that the fire from the lava pit was so intense, neither Superman nor Darkseid could survive it, which means they are both definitely dead. Lois and Jason seek solace in each other as they weep over Superman's loss.
The film, and the series ends, as Earth once again begins rebuilding what was lost to Apokolips, only this time never having to worry about the empire as a threat again. Superman's death is especially commemorated for his own sacrifice; Big Barda agrees to fulfill his shoes as the world's greatest hero, just as Superman wanted her to do anyway, and Lois sinks into depression over her second husband's loss. Jason, meanwhile, decides to literally travel the planet, finding a purpose in his life, as he doesn't feel as if he could fill his father's shoes as Superman. He ultimately ends up at the Fortress of Solitude, where he activates the crystal containing the information provided by Jor-El. Jason asks if he could ever become like his father. Jor-El finishes it all by saying, "Of course; it is as it always will be. The son becomes the father, and the father becomes the son."
A/N: That's it everyone. That's how it all ends. I await your comments.