Let me redo mine.
1. Lex Luthor creates Parasite, and there is a storyline with Braniac (the type from the JLU cartoon, part of the whole Krypton destruction and all that). Parasite is killed, Braniac is destroyed and Luthor is arrested after finding out that Superman's weakness is kryptonite (from Braniac).
2. Luthor and Metallo team up. Luthor has the Kryptonite poisoning and is a villain as well. Metallo is killed and Luthor is arrested.
3. Luthor is out of jail and has felt the power of Superman, so he creates a clone. This becomes Doomsday. Doomsday is eventually killed or sent off to the Phantom Zone, and Luthor is arrested or something.
If there is a way to fit Darkseid in there I'd throw him in too but I don't think I could fit him in there.