In my DCU Doomsday would be an event not the name of the alien and it would be the most destructive event in my DCU. The story would begin much the same as the death of Superman with the creature digging his way to the surface and beginning has rampage. The first hero the creature would encounter would be Hal Jordan who would be killed by the creature. Hal's ring would then go and choose Kyle Rayner to be his successor. Upon receiving the news of Hal's death John and Guy would head to earth to also face the creature. When the Guardians view the footage transmitted by Hal's ring before his death they recognize the creature and order all Green Lanterns to stay away from Earth (John and Guy ignore this order). Ganthet knowing full well what the creature is capable of would chose to leave his brothers and head to Earth himself to aid the heroes there. We next see the creature meeting Hawk & Dove (Hank & Don) he would kill Dove and badly injure Hawk in the fight. More and more of Earth's heroes would encounter the beast and fall at his hands. Red Robin, Superboy, and Wonder Girl would all fall next. Guy Gardner would foolishly challenge the beast and would also be killed as John Stewart arrives too late to stop him. As more of Earth's heroes arrive they make a plan to use all of the heavy hitters to battle the beast up close while heroes with energy based attacks would blast him from the sidelines. The creature would seem almost unstoppable to their attacks with almost no damage being done to him and any injury healing its self before their eyes. Ganthet would arrive and begin to attack the creature doing the most damage with his blast and then an assault from Superman, Mister Majestic, Icon, Zauriel, Wonder Woman, Captain Marvel, and Power Girl would finally make the beast fall. As soon as the beast drops to the ground Zauriel would cut off his head with his Flaming Sword and then plunge it through the top of its skull and the fire would consume the head. Immediately following the death of the creature Amanda Waller would order the Freedom Fighters (see how I would do it Freedom Fighters) to recover the remains and hand them over to the United States Government.
Tired of Superman's interference Lex Luthor would begin to want a Superman who would work for him instead of against him so he would decide to clone the man of steel. His first attempt to clone Superman would become known as Bizarro and it is because of that failed attempt that he decides to combine the Kryptonian DNA he has with his own to try to stabilize the process. The end result of Luthor's Project Superman would be Superboy (who would be about eighteen and who Superman would later name Kon-El). Superboy would have all of his standard powers but because Lex wanted to make him superior to Superman he also has the ability to send energy blast through his hands (like the Eradicator). Superboy would work for Lex for a while and make Luthor Corps. image look good by saving people until he learns the truth about Lex and then he sides with Superman. Superman would eventually learn to trust Superboy and would take him to his parents farm to be raised by them and he would give him the secret identity Conner Kent.
I would keep Static close to the same but I would have him be close to eighteen and I would have it be revealed that it was Lex Luthor who tampered with the gas Virgil was exposed to. Lex would have done this in an attempt to make more Earth born metahumans.
(I wanted to give Amanda a great team that wasn't the Sucide Squad and I also wanted to bring in the Watchmen in some form or another so I decided to combine the two idea.)
After the Justice League of America helps form the Justice League International Amanda Waller feels that they could be training metahumans who could one day attack America. Amanda would turn to her friend General Wade Eiling for help convincing the the United States government that it needs to back a new team one to protect America's interest at home and abroad the Freedom Fighters. Amanda would also put herself in the position to chose the team to get the best results. Amanda's first choice is Colonel Rick Flag wanting him to be the field commander she will give him the code name Uncle Sam. After this Amanda, Rick, and Wade all go to convince Captain Nathaniel Adams (Captain Atom who will seem even more like Dr. Manhattan) to join. Amanda then recruits the street level heroes Question (Vic Sage who will wear brown clothes and maybe a white mask and be as much like Rorschach as possible) Owlman (Roy Raymond Jr who might have less of a connection to Batman) and Phantom Lady (Stormy Knight). Amanda then takes her entire team to the home of Jim McArest and she begins to tell Jim she knows tht he is Mr. Majestic and that he has lived on Earth through all of America's history because she had seen him painted in the Crossing of the Delaware painting. She tells him she knows he fought for America then and that she wants him to fight for America now.
With the number of super hero teams rising around the world the U.S. government decides it needs a super hero team it can work with directly so the choose the Justice League. the united states would Give the Justice League a base of operations in Washington D.C. the Hall of Justice and the team would rename themselves the Justice League of America. Not all of the team goes along with this decision for one reason or another so the founding members of the Justice League of America are Superman, Batman, Wonder Woman, Green Lantern (John Stewart), Martian Manhunter, Mercury (see how I would do it Flash), Aquaman, Firestorm (see how I would do it Firestorm), and the Atom (Ryan Choi see how I would do it Atom). Some time after the Justice League of America is formed Superman would stop an attack at the UN headquarters in New York and there he would be questioned by world leaders as to why the the Justice League is now the Justice League of America. They would ask him if aliens invade the Earth do they invade the whole world or only the US. Superman would then convince the rest of the team to help the United Nations set up the Justice League International. The JLI who gather heroes from around the world and team them with members of the JLA for different missions (think Justice League Unlimited) and that there base would be the Watch Tower orbiting space station. Upon hearing this news Dr. Light would decide to work with the JLI full time to train new members and to represent her country of Japan. The hero know as Icon would be chosen to be the full time team leader and the team would rotate heroes from around the world in diffenent story arcs.
After Barry Allen is killed by Darkseid (see how I would do it Flash). Wally West would become the Flash and after being told by the Justice League not to help fight the New Gods. Wally would turn to Nightwing to help him recruit heroes to help stop the incoming parademons. Nightwing and Flash would contact several heroes and the would fight along side the Justice League and help defeat the New Gods. After the battle the heroes gathered by Nightwing and Flash would form a team and call themselves the Titans. The team would include Nightwing, Flash, Donna (Troy), Superboy, Static, Emerald Dragon (see how I would do it Green Arrow), Starman (Jack Knight), Starfire (she would be way smarter than her outlaws appearance and better dressed too her costume would probably resemble her Teen Titans tv series costume but she will look like her comic book self), (and after the events of Doomsday) Green Lantern (Kyle Rayner).
I would have Diana and Donna be the daughters of Hippolyta and Zeus. The name Wonder Woman is a title given to Themyscira's greatest warrior Diana and this will cause a little rivalry between the sisters. The Wonder Woman costume would look like something worn into battle by Greek warriors (kinda like the WW style costume worn by Lois on the Smallville show) and would be red and black. After the return of the Greek Gods (see how I would do it Justice League) Dianna would become an ambassador to the U.S. and would change the colors of the costume to red and blue. When Diana prepares to leave home Donna volunteers to go with her. Donna would fall in love with America and want to become a hero herself. Donna's costume would be black with red stars (like the one she wore in Titans only not as low cut and I would trade the silver boots with the black and white ones worn by Wonder Woman in the new 52. While in America Wonder Woman would discover that Zeus had come to earth fifteen year prior to the Greek God invasion and fathered another daughter Cassie Sandsmark. Wonder Woman would train Cassie and she would take the name Wonder Girl.
I would do Green Arrow pretty close to how he has been done before. He would be older than a lot of the heroes (40ish) and I would keep his new costume from the new 52. Oliver would have mentored a man named Roy Harper who would be know as Red Arrow but after discovering his drug addiction he would break ties with him. After kicking his drug habit Roy would begin training with other forms of weapons and take the name Arsenal . After parting ways with Roy, Oliver would discover he has a son in Hong Kong named Connor Hawke and he would bring him to America. After discovering his father is a super hero Connor would want to follow in his footsteps and would begin training with Oliver. Connor Hawk would be come the hero Emerald Dragon and would not only use a bow and arrows but also trowing stars and various other weapons.
I would have Jason Rusch be the first Firestorm. Also I would have firestorm be only one person. Another thing I would do is have his powers be limited to flight and flame blast of different degrees but none of the transmuting powers. I would have his costume look like the classic Jason costume not the new 52 version.