As for the Marvel side. I plan to bring the Marvel characters that share the comics and MCU histories since the characters have their powers and origins.
MCU Timeline altered into a different universe.
The story takes place in the MCU chronologically sometime after. X-Men, Fantastic Four, Inhumans, Avengers, Runaways, Guardians of the Galaxy, and Defenders.
Bucky Barnes became Armin Zola's experimentation subject. He was later fell into the river during the mission to captured Armin Zola and HYDRA made him as their personal assassin with the help of the Soviet.
[Spoiler Alert] Red Skull formed the Hydra organization and he will never teleported to Vomit after drop the Tesseract in his own ship and crash, Baron Strucker went in Hydra academy and take the leadership of HYDRA. Strucker created Advanced Idea Mechanics after the end of World War 2. Red Skull was given birth with his daughter Sin with her mother after HYDRA and the Hand revived him.
Nobu Yoshioka was a founder of the Hand and revived to live in centuries until the golden, silver and modern era.
Tony Stark was kidnap by Wong Chu begin saved by Doctor Ho Yinsen with the Mark 1 armor, Bruce Banner saved Rick Jones from he Gamma Bomb and it transform him into the Hulk, Bruce will remain between his human form and Hulk form.
Betty Ross became Red She-Hulk after sometime between the Battle of New York and her death at the hands of Abomination.
Thundra and Bruce Banner gave birth to their daughter Lyra.
Lady Liberators were formed by Thundra alongside She-Hulk which she led the heroine group.
Rick Jones was abducted by Leader and M.O.D.O.K. and mutated into A-Bomb by the DNA of the Gamma-powered Abomination.
The Avengers will share smiliar history of their MCU counterpart.
Scarlet Witch and Quicksilver are the children of Magneto and they have be experiment by the High Evolutionary. They'll became the Brotherhood of Mutants and later join the Avengers after the Battle of New York of 2012.
Peter Parker has been Spider-Man for 8 years which smiliar that of his ps4 counterpart.
Gwen Stacy and Cindy Moon, were bitten by the same radioactive spider that bit Peter Parker by it's dying. Gwen took the mantie of Ghost-Spider and form a group called Web-Warriors. Miles Morales was bitten by the same spider Peter Parker got his powers.
The Spider Society give Anya Corazon a spider shape tattoo that endows her with spider-like powers.
Mary Jane had become Iron Spider because of between her and Peter Parker's on and off relationship, Pepper request Tony to bulit the Iron Spider armor and prove Spider-Man's innocence.
Jackal created the clones of Spider-Man are Ben Reilly and Kaine. Ben Reilly will be remain his mantie as Scarlet Spider. Kaine going to be in his comic appearance.
Doctor Octopus formed the two villainous organizations the Sinister Six and Sinister Nineteen.
Ultron was built by Tony Stark and Bruce Banner instead of Hank Pym.
X-23 was created by the Facility during the Hulk vs. Wolverine movie and later join the X-Men.
Cable organized the mutant group known as X-Force.
Eddie Brock married Ann Weying and moved to New York as they began their own career. Venom bond with Spider-Man on earth and later bond with Eddie Brock after it was debond with Spider-Man.
Venom Symbiote disovered a portions of itself bond with other hosts and fully bonded with Eddie Brock. Anne Weying kept a portion of the Venom Symbiote and live.
Mr. Negative created F.E.A.S.T. the shelter for homeless people and his own criminal group Inner Demons.
Flash Thompson have suffer PSTD due to his experience multiple bondings with the Venom symbiote and Mr. Negative cured his PSTD in order to stop the trigger and he bond with Anti-Venom.
Andi Benton bond with the Mania symbiote.
Life Foundation founded by Carlton Drake and he bond five Klyntar symbiotes from the Venom symbiote to his five employees.
Hank Pym will be Giant Man and Jane Pym will be the original Wasp and have two daughter Hope Van Pym also known as the new Wasp and Nadia Pym as the Red Queen.
Baron Helmut Zemo will take the mantie after his father's death and becoming a new leader the Masters of Evil after sometime the Chitauri invasion of New York in 2012.
All of
Marvel heroes: Avengers, Fantastic Four, X-Men, Defenders, Marvel Knights, Venomverse, Heroes for Hire, Guardians of the Galaxy, the Inhumans, Midnight Sons and more.
Marvel villains: HYDRA, A.I.M., The Hand, Masters of Evil, Sinister Six, Brotherhood of Evil Mutants, the Black Order, the Kree Empire, the Skrull Empire, and more.
Thanos and the Black Order search for the infinity stones and stop by the heroes of Earth during the infinity saga.
DC Universe Timeline
As for the DC side. I also going to bring DC characters Crime Syndicate of Earth: 3, Batman Beyond, and the other alternative universe characters to join the crossover.
Heroes: Justice League, Teen Titans, Birds of Prey, Doom Patrol, Outsiders and more.
Villains: The Society, Legion of Doom, Injustice Gang, Sinstero Corps and more.
This is non canon-story where it takes place after Darkseid's invasion is thwart. Thanos' search for the infinity stones and his regin is ended.
Piot: In the DC Universe, Teen Titans and Justice League have defeated Darkseid and his armies from his conquest of taking over Earth and banish him in the Boom-Tube portal. Meanwhile in the Marvel Universe, the Guardians of the Galaxy and the Avengers have stop Thanos and the Black Order from using the stones to destroyed half of the universe again. Captain Marvel blasted the alien warlord inside the portal he use from one of the infinity gems. Of course, neither one of these are occurrences do not killed Darkseid or Thanos. They both get fused into the monstrosity entity known as Thanoseid and caused a world-merging crisis, pitting DC characters and Marvel characters against each other in a convergence of the two universes. As the Combat Rage become more powerful and the rage is known as "Infinity Rage" setting the rage to make any individuals strong and becoming invisible and strength. Will they work together to stop Thanoseid, or will they destroy each other and both dimensions will be destroyed.
-In the DC Universe-
The city is called Metropolis is invaded by Apokolips led by Darkseid in the arduous battle. The Justice League and Teen Titans managed to fight off his army and went into Apokolips enter the room where he sit on his throne and his elite team are with him. Unfornality, the Justice League and Teen Titans defeated Darkseid and his Elite team by overpowered them, forced Darkseid to open the boom-tube portal and his elite team retreat into the portal. As the elite team make it out of the portal waiting for their master. The Dark Lord said, "This isn't over, League and Teen Titans. Darkseid will destroy Earth and all those who oppose me?"
"Don't be so sure?" Superman said, he use his heat vision to blast at Darkseid and the Dark Lord of the Apokolips said, "The time tube, you stabilized the boom-tube?" They watch as the yellow glowing all over his body, Darkseid gave a final yelled and the portal vanished and cause the throne room collapse. the Justice League and Teen Titans sees the yellow energy flowing away. Cyborg said "I believe he's gone. We should teleported back to Earth?"
"Then make it quick. This place is about to collapse on us real soon!" Green Lantern remind as Cyborg was able to use his weapon tech to make a portal to take them back to their planet Earth.
-Meanwhile in the Marvel Universe-
After the search of the infinity stones on Earth. Thanos sent the Black Order to retrieve them from Earth, but the plan was halted and thwarted. The Avengers and Guardians of the Galaxy stand and fight against the Black Order and Mad Titan Thanos who is empowered by the infinity stones and the heroes manage to end his reign and his invasion of Earth.
The Mad Titan and the Black Order are overpowered by the heroes. Thanos used the space stone to open a portal and called, "Black Order, retreated back to Titans." the Black Order responded to the request and went they make it through the portal. The Mad Titan was last to escape the battlefield so he could fight the heroes another day, Before he could retreat in the portal. Thanos looked back and said, "We will fight against again another day and this will not be over, Avengers and Guardians! The whole universe will bow before me! I will destroy those who oppose me will eliminate"
Captain Marvel replied, "It's not gonna happen?"
Captain Marvel transform her hair and eyes into her Binary form and then charged at Thanos by blast some much from her Photonic energy to where Thanos stands near the portal he uses from the space stone to escape.
Thanos says, "this is cannot be, you stabilize the portal from these stones!"
Thanos yelled in agony as the cosmic energy blasted through his body on the portal. The energy appears changed glowing colors around his body and something's dangerous, the Mad Titan gives one final yell and the portal he uses for the space stone, he is now banished along with the portal explodes and he's finally gone.
The Avengers and Guardians of the Galaxy believed that he is gone and now the heroes farewell to each other and scatter the stones by split across the universe to keep them safe from anybody try to use it. the Avengers are going to their now quinjet to go back to earth, the Guardians of the Galaxy going back to Knowhere.
The heroes believed that It seems that no matter how Thanos is going to destroy all life of the universe and planets who oppose him years ago.
-Unknown Somewhere in between realities-
Unbeknownst to everyone from both separated universes neither of acts do not killed Darkseid or Thanos. They are fused into an unknown entity creature that is resemblance of Thanos and Darkseid. The entity monstroility is called Thanoseid and he becomes powerful, he sees memories of the heroes from both separated worlds defeat them during their conquest in the event moment. Thanoseid still can feel the energy runs through him and using the energy within him and use the reality stone to cause a merging the two universes and he's watch as they are collided.