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.

The answer to why Spider-Man doesn't even cause a ripple in Mayor Fisk's NYC goes back to the end of No Way Home. The Spell wiped out all memory of any connection between Peter Parker and Spider-Man. But MJ in the coffee shop doesn't recognize Peter as a classmate either. It appears that the Spell actually completely removed all memories of Peter Parker.

Consider Peter's situation post NWH, he is completely alone, no friends, no family, no mentor, no support of any kind. He might even have had to get a day job.

But it was his relationship with Tony Stark, with the Avengers, with Nick Fury that Mysterio used to trick Peter and eventually resulted in his unmasking. Peter decided to continue as Spider-Man but could have real concerns about teaming up with other superheroes in the future. So he could be avoiding the other heros in NYC.

He may have even gotten more discreet in his heroing. Sticking to a lower profile as he intercepts criminals. In and out of situations as quickly as possible.

Another factor is Spider-Man's wall crawling which keeps him high off the streets and how quickly and quietly he swings through the city.

There's a possibility that he isn't considered a vigilante because he was part of Tony's team supporting the Sokovia Accords, and may have signed them. Combined this could account for Fisk's Vigilante Task force not targeting Spider-Man.

Matt Murdock's memories of Peter are gone too. He would even remember any relationship with Spider-Man. So he isn't likely to seek him out.

As we wait for the release of the final issue of Ultimate endgame on how the final battle ends, I have my prediction on how the final issue plays out including Ultimate finale

Continuing the final issue , the maker is finally free from his imprisonment and begins his plan to discard the universe , the council and the makers army overwhelm the resistance despite their efforts and Doom (6160 reed) and Tony aka Iron Lad tried to stop the maker but he is considered too powerful and cannot be stopped, that is when Doom  decides to use one last effort, he confronted the maker and then suddenly cosmic power begins to effect both of them and knocked out both, which surprise both sides the resistance and the council and then the maker gets up  but he cause the  Children of Tomorrow to dissolve and weaken the councils security systems causing the resistance to overwhelm them and then  the maker begins  to reform himself into his humanoid form and the maker  removed his helmet and then surprisingly his head is no longer of 1610 reed but the 6160 Reed’s own face.

It was revealed that while being imprisoned by the maker Doom learns a technique of  mind transference from some technologically advanced beings and used it on the maker to switch minds a similar technique from the classic Fantastic Four #10 (1963) which means Reed is now inside the Makers body while the Maker is now inside the body of his useless scarred counterpart that is doom which means he is powerless, in panic the maker use a failsafe protocol  by using a portal to transport himself  back to the ruined world of Earth-1610 before the heroes captured him , with the maker retreat in defat and never coming  back, the heroes are triumphant but at what cost as most all died in the battle against the maker

 

The finale shows the aftermath of the battle, the heroes pay tribute to the people who died including captain America and likely wolverine, It was revealed that Peter aka Spider-man is not dead but crippled which means he is no longer Spider-man, however it is hinted that his son has become the new spider-man , Reed formerly Doom in the makers body is shown using the makers powers to rebuild the world by changing the clones aka children of tomorrow into his helpers to create shelters for the homeless and help deal with the problems in society ,  imprve the continents and make a better, peaceful society.

The X-men are shown leaving in peacefully sanctuary somewhere in Japan similar to Krakoa and help others learn how to use their powers, Tony who after visiting the memorial of his dad Howard abandons his iron lad moniker and calls himself iron man, he is last helping Reed rebuild the world while helping with the increasing membership of the Avengers and also the 6160 of the fantastic four called the Fantastic force in case if any former members of the council of maker or the makers come back to attack again.

 

The last pages of Ultimate finale  takes place in the ruins of Earth-1610, the maker now in 6160 Reed’s Dooms body is raging in isolation because of his defeat by his 6160 counterpart , he then looks at various monitors showing different Reeds from every earth in the marvel multiverse and made a new vow to wipe out every variants of Reed Richards across the Marvel Multiverse and proclaim himself “The maker is dead , Long live Doom” which shows that the 1610 Reed is no longer the maker but Doom instead making him a multiversal threat to the Marvel universe.

And that’s my prediction for Ultimate endgame final issue and ultimate finale, what do you think?

Ok maybe this has been said before so I will keep it short just in case… Maybe Thanos was supposed to win? Think about it, Arishem said that planets are destroyed by the birth of a celestial ONCE THE PLANET REACHES A CERTAIN POPULATION… So, what if Thanos’ indescribable and unexplainable yearning to get rid of half the population of the planet was simply his “Glorious Purpose” meant to ultimately help Earth… the Avengers stood in his way thus prolonging and ultimately undoing it. What’s the timeline on the Eternals? Do they coincide??? I guess I could look this up but I wanted to get the thought out into words before scrolling removed my desire to. Just watched Inginity war for the hundredth time and it dawned on me… had to ask!