Doomsday plot leak from 4chan
Backstory:
The Incursions are happening because Earth 616 (MCU) and Earth 10005 (X-Men) have interfered too much with the multiverse
616- they messed the timelines in Endgame to revert Thanos actions. Then Spider-Man and Strange almost broke the multiverse, and Wanda almost caused an incursion
10005- they messed the timeline with the time travel in DOFP, and then they rebooted the timeline again at the end of Deadpool and Wolverine
In Doomsday they lean into the parallels of MCU and Foxverse. Because of their actions, even though they had good intentions, their universes have become unstable and have started multiple incursions with other universes
The film begins with the X-Men universe having an incursion with Tobey Maguire Spider-Man universe. Wolverine fights Spider-Man and succesfully puts a device created by Beast that destroys Tobey's universe. That way, X-Men universe survives, but Wolverine dies alongisde Tobey's universe.
Charles Xavier and the rest of the X-Men mourn his death. The X-Men team is the same we've seen from the posters and trailers but there's also Deadpool. They mention that Storm and Jean Grey died trying to stop other incursions. The X-Men are tired and horrified by the act of killing a universe, but it's the only way to survive.
On Earth 828, Reed Johnny and Ben are attending a baseball game. Sue calls them. They arrive at the Baxter Building and they meet Doom. Reed is the only one that knows him, they met in college. Sue only knows him as the dictator of Latveria, and resents him for that. But Doom says that thanks to him, Latveria is better than ever.
Doom explains that he has spent years investigating the multiverse and has discovered that their Earth 828 is about to collide with other 2 earths. He asks Reed if maybe there are people from other universes living in 828. Reed tracks the house of Steve Rogers.
They meet Steve and he explains that he used to live in a branch timeline of 616, but Loki appeared and told him they were going to prune the timeline, and gave him the chance to live in a completely different universe: 828. Steve and his family have spent 10 years living in 828, and have seen the rise of the fantastic four and their fight with Galactus. The son of Steve, James, is a Big fan of the FF and he loves their cartoon.
Steve, Doom, and the FF travel to 616. The incursion has started and space starts to break. That's the space crisis that was mentioned in the Thunderbolts post credit scene. Love, the daughter of Thor, has a vision of death, and when Thor sees the space crisis, he travels there. Thor finds the FF ship and he meets everyone, including Steve Rogers, who grabs the mjolnir to prove it's him.
The FF ship arrives at the Thunderbolts tower and Sam's team also arrives. It's only Sam, Joaquin and Scott Lang, because Shuri is in Wakanda. Joaquin is very excited to meet Ant-Man, as he mentioned in Brave New World. Sam and Bucky have a few quips and clashes until Steve convinces them to work together. Scott also meets Ghost and is happy for her.
Reed explains the situation. 3 universes, 828, 616 and 100005 are about to collide. They debate what to do. At the end, Reed proposes to use cannons to separate these 3 universes. But they need very advanced techonology, so one team travels to Wakanda, and the other travels to the X-Men universe to ask them for help. Meanwhile, Steve and Thor travel to the TVA because Steve has a card that Loki gave him.
In Wakanda, Shuri has already seen the space crisis and asks Namor for help, but he refuses. Sue meets Shuri and Namor, there's some romantic quips from Namor but Sue doesn't like him. The other team travels to the X-Men universe and at first they fight (it's the battle we see in the trailer). At the end Monica Rambeau stops the fight. They talk and they realize they want the same thing: to stop the incursions.
In the TVA, a weakeaned Loki reunites with Thor and Steve. He tells them that Doom has stolen his powers and now he is unstoppable. He wants to destroy the multiverse so he can create a new perfect universe. Steve and Thor travel to X-Men universe and reveal that Doom is evil. Doom activates the sentinels and the Avengers and X-Men unite to fight them. The sentinels destroy the mansion and Thor tries to attack Doom but he stops the attack with two fingers.
After Doom defeats everyone, he travels to 616 and kidnaps Franklin from Sue. She tries to stop him but he escapes. Doom wants to use Franklin's powers to destroy everything, because he has the cosmic power of Galactus. Doom also kidnaps Steve.
The sentinels keep attacking the heroes and they hurt Yelena. That angers Bob and he becomes Sentry. He destroys the sentinels but starts attacking everyone else. Xavier enters his mind and defeats him. Then, Xavier uses Cerebro to locate Franklin in the multiverse, because he's a mutant. He's locked up on Doom's Castle in Latveria.
In Latveria, Doom explains to Steve his backstory. He investigated the multiverse since he was young because he wanted to find his deceased mother. But instead of that, he found love. He met the Sue Storm of another universe and had a kid with her. But because of that, he caused an incursion and when he tried to stop it, he accidentally killed his wife and kid. His face was disfigured from that moment and that's why he wears a mask.
He thinks it's unfair that Reed has the life that he always wanted, and also that Steve got to break the rules and have a son in another universe while he couldn't, and that is the reason why 828 is having an incursion with 616. Because of that, he kills Steve's son right in front of him, for "justice".
We see that Dr Strange and Clea work for Doom. Some years prior, Dr Strange and Clea tried to stop the incursion between MCU and Earth 838 (Illuminati universe). They tried everything but failed. Then Dr Doom appeared and made the difficult decision to destroy Earth 838, because if Earth 616 got destroyed, the entire multiverse would collapse because it's the sacred timeline. Doom, Strange and Clea investigated the multiverse until Doom realized the only way to be free was to destroy the sacred timeline and start anew. He possesed Strange and Clea so they would become his henchmen.
The Avengers, the X-Men and the FF travel to Latveria as the incursion starts to happen. Sue tells Reed that she is pregnant again, and Thor asks help to Odin. Warriors from Valhalla appear. Odin, Heimdall, Jane Foster, and the Loki from Infinity War. Reed enters Doom's Castle and rescues Steve, and he tells him everything.
There's a Big Battle between the heroes and the Doombots. Reed, Cyclops and Sam Wilson fight Dr Doom, and after they defeat him, they realize he's only a Doombot.
The real Dr Doom is outside the multiverse with Franklin. He has tricked everybody. Doom absorbs Franklin power to destroy everything. The entire reality collapses. Everyone dies. Doom creates Battleworld. Sue is his wife, Franklin is his son, and Doom has adopted Reed's new child, Valeria.
In the post credit scene, it's revealed that the only heroes who survived and remember everything are Tobey Maguire Spider-Man, Hugh Jackman Wolverine, Tom Holland Spider-Man and the Young Avengers.