Start with Green Lantern and then add Man of Steel. Finish with Justice League.
Amanda Waller works for DEO in the Green Lantern, not Checkmate, so this should be pretty easy. Destroy Luthercorp all in total and make Lex Luthor the president of DEO and the man in charge of the subcommittee that placed Hector Hammond in charge of dissecting Abin Sur. Then have Hal vanishr from Earth to explore the sector and protect it.
Here's where Clark comes in, he becomes Superman and when Luther realizes that Clark is an alien. Associate it with Abin Sur, whose body is taken by the Corps, but Luther believes it to be Clark, protecting all aliens. After Superman becomes a hero, he is confronted by Hal and bam, Flash arrives.