This is a pure fan theory, I added things that are not confirmed. I did use AI to polish it and organize it, but the theories is fully mine (So if you see weird word uses, don't blame me).

Pre‑Film Setup

Spider-Man: Brand New Day — Post‑Credits Scene

• Doctor Doom sits masked upon a throne in Doomstadt.
• Flashbacks reveal young Victor von Doom and Reed Richards growing increasingly hostile toward one another. Their rivalry grows around intellect, ambition, and Sue. During an experiment gone wrong, Victor becomes scarred.
• Present day: Doom walks through his castle and enters a chamber containing a massive map of the multiversal tree. He studies it silently.

Fantastic Four — End Credits Tease

• Shows Doom holding Franklin Richards with his mask off

PROLOGUE

• Earth‑828: Six‑year‑old Franklin Richards plays with Ben Grimm. Nearby, Reed, Sue, and Johnny speak quietly. Reed has discovered evidence of the multiverse and fears Franklin possesses immense power beyond their understanding.
• The End of Time: Doom enters a laboratory, equips newly forged gauntlets, and opens a portal.
• Loki sits upon his throne sustaining the branches. Doom approaches. Loki senses him.

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• Doom deploys a power-siphoning device, bleeding Loki's energy out slowly to harvest it. Doom overpowers and defeats the weakened Loki, who barely escapes.
• Without Loki fully sustaining the throne, the multiversal branches begin a slow, agonizing decay. Across realities, only hours remain.
• Marvel Intro: Cracks spread violently across the logo.

ACT I

Earth‑616 — Status Update

• Wong oversees the completion of New Kamar‑Taj, headquarters for a future Avengers initiative. Sam Wilson, Shang‑Chi, Scott Lang, Hope Van Dyne, and others assist.
• Meanwhile, Peter Parker swings through New York. Matt Murdock and Frank Castle fight crime on the streets. The Thunderbolts establish themselves at Avengers Tower.

The Warning

• Doctor Strange and Clea return from the Dark Dimension with terrible news: Incursions are accelerating, and the multiverse is collapsing.
• Thor arrives carrying his ill daughter, Love. Wong explains she is already feeling the universe dying; saving Earth means saving her.

Other Worlds

• Fox X‑Men Universe: Incursions approach. The X‑Men have built a machine capable of destroying another Earth to save their own. The team is divided, but desperation wins.
• Raimi-Verse (Tobey Maguire's universe): Peter Parker is married to MJ, and their daughter Mayday exists. Peter hears panic outside as another Earth appears overhead.
• Reality tears apart. Peter discovers the X‑Men deploying their machine. He fights them, loses, and races home, reaching his family moments before his universe dies completely.
• Earth‑828 Falls: Reed activates a machine designed to save both universes during their own incursion. It fails. Earth‑828 begins collapsing. The Fantastic Four flee aboard a ship just as Doom opens his own portal, his army following close behind.

ACT II

The Gathering

• Loki arrives on Earth‑616. The Avengers prepare for war.
• The Fantastic Four arrive and explain who Doom is. Loki explains that time moved differently at the End of Time; the branches are decaying, and Earth‑616 only has hours left.
• Loki reveals Doom's true objective: Capture Franklin Richards, harness his reality‑warping power, destroy the dying multiverse, and create a new stable reality in Doom's image.

Reed and Doom

• Before the battle, Reed confronts Doom via a holographic transmission.

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The First Battle

• An incursion begins. The desperate Fox X‑Men arrive and deploy their machine. The Avengers and Thunderbolts attack. The X‑Men lose, and the machine is captured, but the incursion still advances. Loki uses his remaining magic to slow it down.
• Doom arrives. Doombots flood the battlefield. Sorcerers, the Fantastic Four, Avengers, Thunderbolts, and X‑Men all fight. The heroes are overwhelmed and forced to retreat.

New York

• Peter Parker hears the chaos and arrives too late. Loki lies dying on the ground, Doom standing above him.
• Peter attacks but is easily swatted away. Loki smirks, revealing a final contingency: he has brought a Captain America suit superjuiced by the raw, fading energy of the dying multiverse. Steve Rogers is the backup plan.
• Loki dies.
• Doom lifts Peter by the throat. During the struggle, Doom's mask breaks. Peter freezes.

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• Doom casts Peter aside and leaves. Peter breaks down emotionally as Matt Murdock and Frank Castle arrive to help evacuate civilians from a collapsing New York.

ACT III

Wakanda

• The heroes regroup. With Loki gone, the incursions accelerate rapidly. Reed upgrades his survival machine using Wakandan vibranium, successfully slowing the collapse.
• Doom appears outside Wakanda with his entire army behind him.

Second Battle of Wakanda

• Wakanda joins the fight. The combined armies make a final stand. Steve Rogers arrives, wearing the multiverse-juiced suit, and charges into battle alongside Sam Wilson and Thor.
• The tide feels like it's turning, but Doom is unstoppable. He overpowers Steve.
• Seeing the line break, Bruce Banner steps up. He engages Doom in a brutal, desperate hand-to-hand fight, mirroring his old clash with Thanos. Doom ruthlessly executes Banner.
• Thor witnesses Bruce's death. Blinded by absolute rage, Thor lets out a deafening roar and charges at Doom with everything he has.
• Right before Thor's hammer connects, Doom coldly teleports away, leaving Thor swinging at open air—utterly denied his revenge.

The Fall

• Doom materializes inside the Wakandan facility. Franklin is guarded by Ben Grimm and Johnny Storm. Ben attacks, but Doom destroys him. Johnny is thrown aside, and Doom seizes Franklin.
• Outside, Doom’s ships open fire. The Wakandan castle crumbles, and Reed's machine is permanently destroyed. Doom escapes into the rift.
• The remaining heroes stand in stunned, broken silence. The sky tears apart completely.
• Yelena Belova looks toward Bob (The Sentry), an idea forming in her mind for survival. Peter Parker stares upward at the burning sky as a single tear falls.
• Cut to black. The horrific sound of tearing reality echoes, then fades into silence.

Post‑Credits

• The End of Time: Doom sits upon the throne once occupied by Loki. Franklin rests on Doom's lap
• The last decaying branches of the multiverse collapse into nothingness. Doom watches the darkness silently.
• Cut to black.