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Deep Blue Day begins four years after the events of Spider-Man: No Way Home, with Peter existing on the edges of a life he no longer belongs to. The narrative opens through Watching You Without Me [Kate Bush], framing him as a ghost haunting his world — present, watching, but unable to connect to anything he once knew

“There is a ghost in our home, just watching you without me.”

He watches MJ and Ned from afar, grieving not only the people he lost, but the version of himself that existed beside them. In Cranes in the Sky [Solange], Peter buries his pain through his work, with endless patrols and upgrading his tech.

“I tried to keep myself busy… ran around in circles think I made myself dizzy.”

Spider-Man has consumed Peter Parker completely. He is numb and his exhaustion feeds his bitterness making him increasingly unwell Didn’t I [Darondo]:

“Didn’t I do the best I could? Didn’t I give you everything?”

Then hope appears unexpectedly. In Will I See You Again [Thee Sacred Souls], Peter encounters MJ and Ned again and discovers they now live in his apartment building. The smallest possibility of reconnection awakens him.

“I got a little taste of your love the other day… and I just can’t get enough.”

But the wound deepens when he sees MJ moving on with her life in I Can’t Stand the Rain [Ann Peebles]. Her future is bright and meaningful — and because of his own choices, he can never be part of it.

“Do you remember how sweet it used to be.”

Across the room she kisses her boyfriend, while Peter remains the friendly neighbour.

A distraction comes with the arrival of Adriana Soria, the Spider Queen, introduced through Cool Cat [Queen]. She is seductive, intelligent, dangerous, and immediately recognises Peter’s isolation. She draws him into a conspiracy involving a mysterious high-value shipment capable of destabilising New York’s criminal underworld.

“You really know how to set the mood.”

Peter believes he is investigating the operation, but in reality he is already trapped inside her design. MJ and Ned begin independently tracking the same pattern of escalating crime and vigilante activity, while Frank Castle (the Punisher) watches from the shadows, convinced something far worse is unfolding.

Everything collapses during the heist sequence in Lebanese Blonde [Thievery Corporation]. Peter’s senses fail him mid-battle. He is struck by Scorpion’s venom, which bonds with something already fractured inside him.

“Too low to find his way… too high to understand why.”

The venom becomes more than poison. It manifests physically from Peter’s grief, repression, isolation, and exhaustion. Through Dreamer [Kelis], hallucinations consume him as his spider side begins mutating beyond his control.

“Every thought shoots like a dart…”

The city turns against him. False narratives spread online and through the media, framing Spider-Man as part of the chaos. In Into Nirvana [Maverick Sabre], Peter becomes hunted by the Punisher, the Department of Damage Control, and secretly, the Spider Queen herself.

“So then I go and run away.”

Seeking answers, Peter turns to Dr Bruce Banner, who confirms the horrifying truth: Peter’s DNA is mutating. The spider side is overtaking Peter Parker completely. Without an antidote, he may lose himself entirely.

At the same time, MJ edges closer to the truth. In I Want by Mk.gee, she confronts Spider-Man on the rooftop, having pieced together the criminal conspiracy herself. She wants to expose whoever is orchestrating the chaos and asks Spider-Man to work with her.

“You’re the best thing I know.”

Peter desperately wants to trust her, but cannot reconcile who she sees with who he believes himself to be.

The Spider Queen escalates matters in The Smoke [The Smile]. After helping Peter defeat Scorpion, she kisses him, transferring more venom and accelerating the mutation. In Cherry [Chromatics], she reveals the truth: Peter was never her ally. He was always her target.

“What Peter thought was connection was control.”

She tells him he can never truly be both Peter Parker and Spider-Man. Human love is incompatible with what he is becoming. Yet despite how deeply her manipulation resonates with his fears, Peter refuses to surrender.

The Punisher becomes the voice grounding Peter back to reality. In Be Thankful for What You’ve Got by Massive Attack, Frank challenges Peter to stop obsessing over what he lost and recognise what he has.

“You can still stand tall… just be thankful for what you’ve got.”

Peter realises his isolation is destroying him. He decides the only way forward is honesty. Inspired by May and Ben’s memory in Umi Says [Mos Def], he prepares to confess everything to MJ.

“I wanna tell you how I feel right now… tomorrow may never come.”

But before he can, the Spider Queen attacks again. During Got Till It’s Gone [Janet Jackson], she lashes out violently after Peter rejects her. In Sowa [Fatoumata Diawara], Peter is psychologically “unmade.” Spider-Man and Peter Parker are erased, leaving behind only instinct and mutation.

His rebirth begins in No One’s Watching Me [Ezra Collective]. Peter awakens cocooned in webs, transformed into something closer to Man-Spider than human. Freed from memory and guilt, he moves through the city with instinctive power in Green Onions [Booker T. & the M.G.'s].

Then MJ finds him.

In Opendoors [Jitwam], she finally confronts the truth he’s been hiding. Peter expect rejection. Instead, MJ refuses to leave.

“I will open doors ’cause I believe in ya…”

Together with Ned and Bruce Banner, she becomes his anchor against the Queen’s influence.

The climax unfolds during the prison break in Slow Tonight [Tom Misch] and Witches Alice [Phoebe Lou]. The Spider Queen attempts to fully merge mutating Peter into herself through seduction and psychic control.

“You’ve got this golden way of making my body sway…”

Peter begins dissolving into her world — until MJ reaches him. Her voice cuts through the trance, reminding him who he is. Hulk’s recognition and Ned administering the antidote stabilise the mutation. For the first time since the beginning, Peter is remembered.

Recognition becomes his restoration.

But the final act pivots toward the truth. The Spider Queen exposes Peter’s greatest secret: he chose to erase himself from MJ and Ned’s lives. He lied. He betrayed them. In It’s All True [Tracey Thorn], Peter finally stops hiding.

“This is just my heart laid bare.”

MJ slaps him and walks away, overwhelmed by the weight of the confession. Yet the story ultimately circles back toward love. In Don’t Delete the Kisses [Wolf Alice], Peter confesses openly:

“I love you.”

MJ initially resists. She is in another relationship and hurt by Peter's betrayal. But in Underwater Love [Smoke City] and Idol Eyes [Common Saints], the emotional dam finally breaks.

“Why did you do that, Peter?”

They kiss and choose each other in Brown Sugar [D'Angelo], before softening into hope through Golden [Jill Scott] and Ascension [Maxwell]. Peter briefly believes happiness might finally be possible.

But Last Dance [LEISURE] introduces the final dread: the mutation and Peters full transformation was never truly finished.

“Can I have this last dance with you.”

The story ends with Under Your Spell [Desire], where the symbiote emerges and takes hold of Peter

“I don’t eat, I don’t sleep, I do nothing but think of you.”

Peter is consumed. And this time, he doesn’t resist or come back.